Jetsetter's SN95 V6 to 4.6 V8 Swap Guide


Active Member
Jetsetter's SN95 V6 to 4.6 V8 Swap Guide

The perpetual question of to swap or not to swap bounds the halls of Mustang forums since illiterate high schoolers have been losing street races in V6's at the dawn of time. Some key points to note is that yes it is cheaper to buy the car you want, especially with New Edge GT values tanking and 99/01 Cobra's and Mach 1's being decidedly affordable thanks to their age. However, especially if you have a wrecked donor car, the swap is very much doable and, in my case, the sentimental side of finally adding balls to the car I had owned since I was 15 made it worthwhile.

In the interests of disclosure, I am a relatively amateur mechanic, but I received a lot of trained help that made the process much simpler from people at my parents transmission shop. I had access to a hoist, industrial air compressor, and a plethora of tools. I simply can't remember every tool I needed, and you will likely have to find solutions to problems that don't have obvious answers. Think critically, you've already been able to read two paragraphs.

Furthermore, I did not deal with the electrical side of the car. PATS retuning, cutting and splicing wires, and finding grounds and all that jazz was done by an electrical shop. My car required a lot of attention to run correctly on the electrical front, as I had to go through three computers, reflashing the PCM, and diagnosing issues. Had I stayed within the electrical guidelines as below, I would expect those issues would be minimized.

If you have differing information regarding this swap, please let me know. I do not purport to be 100 percent accurate, and my memory has started to fade since the process began.

The car I started with is a 2003 V6 Mustang with an automatic transmission and a 7.5 rear end. I did not have the TCS or ABS options. I had made no electrical modifications to the vehicle, nor any performance modifications other than a butchered stock exhaust with dual Flowmasters and aftermarket headers.

The engine I was to swap was a 99 Cobra DOHC 4.6 with a T45 transmission. I did not have a donor car, but had many of the necessary parts off of the original car, including an engine complete with with most accessories. and emissions plumbing.

You pull it style yards have been helpful in finding parts necessary for the swap. The 2V found in the GT can be also be found in the:

Crown Victoria
Mercury Grand Marquis
Lincoln Town Car

While the 4V's can have parts scavenged from the:

Lincoln Mark 8
Lincoln Aviator

Not everything will match, but for bolts and accessories, these are your lowest cost options.

Things You Need

This is for the V6 to 4V 4.6 arrangement, parts needed for other swaps may vary.

An engine - No idea how to build a 4.6, so lets start with the whole entity. You need an engine with a throttle body, throttle cable bracket, EGR valve and bracket, EGR solenoid and bracket, idle air control valve, plugs, injectors, PCV tubes, fuel rails, and fuel pressure sensor.
An engine harness - There are 4 significant harnesses on the car - the engine harness, the transmission harness, the dash harness, and the body harness. I mixed a 99 engine and trans harness with an 03 dash and body harness, and yes it required cutting.

I'm an advocate of trying to match your engine harness to the year of your dash harness, so you do not have to chop up the wiring or replace the dash harness. 2V's should be easy to match as GT's were produced the entire duration of the body style. If I could do it again I would likely get an 03/04 Mach 1 engine harness for my 99 Cobra engine, which I understand are identical except that the Cobra has knock sensors in the engine valley with the Mach's do not have. After turning off the knock sensors in the tune, I wouldn't have had to cut the wires on the engine to dash harness. While I can't read electrical diagrams because I'm stupid, my trips to the junkyard showed me that certain years of cars were more like each other and would've caused less issues during the final wireup.

99/00 are similar
01 is unique
02/03/04 are similar

Almost all of the electrical work had to be done down in the passenger side footwell where two of the three engine to dash connectors were the same and one did not fit. A cut connector from the engine harness of an 02 V6 was soldered onto the 99 engine harness to allow it to be plugged into the 03 dash harness.

To reiterate, I have a strong preference for continuity in electrical systems, especially for the uninitiated. If I had spent a little more on eBay buying the same year harnesses, I may have saved myself a year of my car sitting outside at the electrical shop. The engine harness is IMHO much easier to replace than the dash and body harness, and I would try and buy the right engine harness for your year of car rather than swap the dash and body harness.

Your engine harness should be complete. Follow it while it is off of the car and check for missing ends if it is used. My engine was in a wrecked car, and I found that several connectors were ripped off. A lot of the electrical connectors between the V6 and V8's are the same, even including the same colored wires. Many of my broken V8 connectors were replaced with snipped ones of junkyard V6's.

You'll need the new power distribution box, which should come with your harness.

It is my understanding that a 4V swap can utilize a 2V harness with the polarity (read cutting and switching the two wires) reversed on the COPs. This may prove to be easier to find than the corresponding 4V harness.

Gauge Cluster – I can’t tell you the magic that goes to making the gauge cluster work, but I got an 01 Cobra one for a deal and I’m using that. Match the cluster to the dash harness based on the rules above.
CCRM – This box goes under the passenger side fender. Take the fenderwell liner out to get to it, not the fender itself. This apparently controls a bunch of engine functions. I’m using one out of an 03 GT. I believe 99/00 are their own style.
Power Steering Pump - My engine came with a power steering pump, but I think these are mostly interchangeable between 4.6's of similar vintages.
Alternator - The 4.6 has a different alternator and you will need the appropriate one for your engine.
Hydroboost - This is a big change between the V6's and V8's. The vacuum assisted brake booster on the V6's is too large for the V8's, and you will need a V8 (Cobra and GT's are the same) hydroboost unit. Do note the 96-98 Hydroboost's are different than the 99-04 Hydroboosts. Either may work on your car, but the lines will have different sizes. It is best to stick with your generation if you're SN or New Edge.
Hydroboost Lines - There are three hydroboost lines that complete the power steering circuit. As mentioned above, use lines from the same body style that you have to ensure proper fitment. I found that the power steering line hookups on my V6 were the right size to fit the V8 hydroboost lines. These can be a pain to find, as every asshole who pulls a Mustang engine decides to cut the lines instead of taking the 20 extra seconds to unbolt the line like a civilized human being. The next time you’re at the junkyard, please think of your fellow swapper and remove them like a big boy.
Brake Pedal Box - A necessity for the transmission swap, you'll still need a GT or Cobra version for the V8 swap, as the hoop that comes out of the hydroboost to connect to the brake pedal is a different diameter on the V6. You can also cut and weld it, but finding a manual GT isn't the hardest thing in the world.
Motor Mounts - These are the same whether you have a GT or a Cobra, but are different than the V6's.
Power Steering Pump Reservoir - These are different. I got mine off of a Mark 8, which had the correct bracket to fit the 4.6 bolt holes on the timing cover.
Coolant Crossover Tube (Cobra Only) - These bad boys cost big time, so I bought one off of a 98 Cobra. I already knew at the time there were going to be issues, as on the 96 to 98's the tabs for the crossover attached to the intake manifold, whereas on the 99 up they have tabs to mount to the alternator. I hammered the manifold fitting tabs to meet the alternator, and while it isn't pretty, it saved me a bunch of money. Someone who could spend 2 minutes welding could make this look good.
Alternator Bracket - This overpriced piece of metal is hard to come by and apparently worth 80 bucks. I got two pieces of scrap metal and drilled holes in them so that the alternator attaches to the intake manifold like intended.
MAF – It’s a different diameter, I think I’m using a GT one.
PCV Hoses – I believe these are different than the GT, I think I robbed what I was missing off of a Mark 8.
Air Intake Tube and Pickup - Different than the V6's, these are easy to find aftermarket or someone selling their stock one who put a new CAI on their car.
Radiator Fan Fuse Box - This is located on the passenger fender. The car is already tapped to bolt it in, and if not just grab a bolt bracket from the junkyard that you got off of a body panel. Your engine harness will have a plug for it.
Radiator - You know, I don't actually remember swapping it, but I'm pretty sure they're different. I think a GT/Cobra one is interchangeable.
Thermostat Housing (Cobra only) - The 4V's have a remotely located thermostat and housing that hovers between three coolant tubes. You will need a Cobra or Mach 1 specific version, as the Lincoln type does not have the correct output angles. An 03/04 Cobra thermostat housing has a third, different type of design that will not work either.
Coolant Hoses - There are four main coolant tubes, one that runs from the passenger side crossover tube to the passenger side radiator, one that runs from the driver side coolant crossover to the thermostat, one that runs from the lower driver side engine to the thermostat, and one that runs from the thermostat to the lower driver side radiator. Additionally there is one that runs from the top of the coolant reservoir (or degas bottle, whatever) to the radiator, although I believe I used the small hose for that from the V6. Most of the hoses were in stock at Carquest, except for the special molded one that had the side tube to the bottom of the reservoir. The Cobra one is discontinued, but I ordered a Mach 1 version that worked fine.
Coolant Tank/Degas Bottle - The GT and Cobra versions are the same, grab one from a GT. There's another version floating around out there, but you need the one with a coolant level sensor molded into the corner.
AC Compressor - My engine came with one, but I believe they are shared among the 4.6's. There are differences in the hookups for the lines between the 96-98 GT's and the 99-04 GT's.
AC Lines - There are 3 AC lines in the circuit. The first goes from the compressor to the condenser, the second from the condenser to the black bottle thing, and the third from the black bottle thing on the passenger side firewall to the compressor. 96 to 98 GT's have a different style bolt on line connector, while the 99-04's have a press on type that click together. Additionally, the 99/00's have a different connector style sensor on the compressor to condenser line, but you can pull the correct year of sensor off of a V6 to match your harness. I’m using the black bottle thing from the V6, the other two lines were pulled from GT’s.
Exhaust - Your V6 exhaust will not work. I used stock headers because long tubes are annoying. As I am using a solid rear axle assembly, the Cobra exhaust would not work. I used a 99-04 GT stock H pipe and some Borla exhaust out of the back. The GT H pipe fit the engine fine.
Exhaust Hangars - Your V6 ones are set for only on side. There are differences between the hangars for the 96-98 GT and the 99-04 GT, so depending on what your exhaust that is going on the car is off of, match the years accordingly. I am running without tail pipes right now as I have to find the proper exhaust hangar off of a 99-04 GT.
Starter – I think these may be shared among GT’s and Cobra’s, but you will need a 4.6 version no matter what.
Vacuum hoses – The vacuum hose harness is red and goes on top of the engine. I’m using a GT one on the Cobra engine, and while it looks horrible all of the hoses connect correctly. I’m going to go back and shorten the hoses and make it look nice at some point in the future.

The other element of the swap was switching out the transmission from a 4R70W to a T45. In short order, the transmission options of SN vehicles are:

96-98 GT - T-45
96-98 Cobra - T-45 with special trans mount location
99-February 01 - GT T-45
March 01 - 04 - TR-3650
01 Cobra - TR-3650

96-98 GT - AODE
99 -04 GT - 4R70W

I can't tell you what will jive when it comes to automatics, but lets be firm that your V6's T-5 is not going to work and you will need either a T-45 or a TR-3650. My preference is for the TR-3650 as I have T-45's in my three Mustang's and they all rattle like Mexican jumping beans during a plane crash, and you have to put them into 1st before going into reverse.

You DO NOT need to cut the trans tunnel out or the hole where the transmission goes. Whoever posted that has probably doesn’t live in a country where Ford cars are sold.

Transmission - This will include the shifter and the little rubber guard that the shifter handle goes through.
Flywheel - Okay, flywheels are a bit complicated. 99-February 01 GT's with T-45's have a 10.5 inch flywheel, which then became an 11 inch flywheel in February 01 onwards with the TR-3650. However, 99 Cobra's came with a T-45 and an 11 inch flywheel. You might be able to mix and match, as long as your clutch kit is for the right size flywheel. The differences in a 6 bolt vs. an 8 bolt are covered elsewhere on the internet.
Clutch Kit - You're on your own to decide from the multitude of options out there what clutch will be your preferred choice. I have used Luk Pro-Gold's in two cars, which has handled some really abusive driving at the expense of a stiff clutch pedal. I have an Exedy Mach 400 that only American Muscle sells in the engine swap car that is sufficiently firm. Just make sure you're getting it for the right flywheel. One more piece of advice, do not use an Autozone or equivalent parts store clutch kit. They are crap, because they are made up of cheap components that often don't match well. Stick with NAPA, Carquest, Pep Boys (not cheapo brand), or your preferred online retailer for your purchase.
Pedal Assembly - This is covered above, but obviously you'll need the whole new assembly. There is no drilling needed to install the new assembly, it's all bolted.
Trans Mount - I saw a variety of different transmission mounts at the junkyard, but primarily there is the wide type that slots into flanges on either side of the transmission tunnel that was on 96-98 GT's and the in the tunnel type mount that is much narrower and bolts closer to the transmission itself. I think I actually used my V6 automatic mount which was the wide style like the 96 to 98 GT's, as the bolt holes lined up for the mount without any drilling. Either way, match the transmission mount to the style of attachment, there is a solution for both types.
Driveshaft - I did not use a Cobra IRS, so I used a T-45 driveshaft. I'm not sure if there is a difference between the TR-3650 and T-45, but I would just match the driveshaft with the transmission.
Transmission Dust Plate – There is a transmission dust plate that goes between the back of the engine block and the bellhousing of the transmission. I accidentally used the automatic plate which left a gap in the bottom of the plate where you would typically twist the torque converter. I remedied this by getting an automatic torque converter cover off of a C6 transmission from the junkyard that bolted right up with no modification.
Clutch Cable – I ordered a new one from Ford because they’re decently cheap and every one of them at the junkyard was cut.

Rear End
I know people enjoy sharing their love of the 7.5 rear end and swear they've ran 9's on a stock one, but 8.8's aren't hard to find, theres a lot more potential there, and I don't feel like I'm maxing out my 7.5 which will explode and leave me stranded. If Ford decided the 215 HP of the non-PI GT warranted the extra cost of an 8.8 rear end (and Ford only spends money when they have to) then I think thats validation you should get an 8.8.

I should also mention I stayed with a solid rear axle (SRA). I know IRS is supposed to be wonderful, but I didn't need the work of finding and grafting one onto the back of my car when an 8.8 does the same job and I can get a panhard bar for it and it will drive better.

Your SRA junkyard parts can come from:
Foxbody Mustangs: These have the narrowest track and are frankly kind of old, but there's nothing stopping you from using one.
SN95 GT's: These have a .75 inch wider track each side due to longer axles, but the housings are the same as the Fox.
99-04 GT's: My personal favorite, these have an addition .75 inches each side over the SN's and 1.5 inches over the Fox's due to longer axles and a longer housing. My preference is for the longer housing as it plants the car better I believe and the wheel will fill out the fender better.

You can use the stock V6 control arms, sway bar, brake calipers, brake lines, and shocks when swapping it out. You really just need the completed axle assembly to bolt in.

Things You Do Not Need
An annoying element of reading threads online is there is a ton of speculation as to which parts you will need for the swap, with some people who didn't know the difference between their car and their butthole offering engine swap advice. You will NOT need the following:
K Member - 96 to 04 they are all the same
Radiator Fan - my V6 one plugged right in to the engine harness
Throttle Cable - my V6 throttle cable reaches to the Cobra's hook up snugly
Cruise Control Cable - while slightly too short to fit into the throttle cable bracket, you can ziptie the cruise control cable to the bracket and still have enough slack to get to the hook up
Brakes - still using the same stock V6 brakes and haven't died as of the time of writing
Fuel tank - fuel tank works exactly the same
Fuel lines - identical too, still using the stock V6's. My fuel line from the tank plugged directly in to the one to the fuel rails.
Suspension Items - you're in the engine bay, not under the car
Steering Rack - It's the same.
Condensor - Same size AC line input and outputs, plugged right into my new lines.

I may update this once I have the car back in my possession and feel it necessary to take pictures. And if you own a wrecked 03 Cobra and would like me to write up a swap guide on that platform, please let me know, because I would like a free 03 Cobra drivetrain.

This post may not be sold, redistributed, modified, or reposted without my express written permission, but if you ask really nicely I’ll probably say yes.


whoa... that's a lot... i'll stick with my 6'er.

and yea i've seen 7.5 rear ends blow at 400 rwhp.

nice write up! pics?


Active Member
It really isn't a lot when you're going to the junkyard, and you figure that everything in essence bolts up. The wiring is the most daunting part to me, and a lot of hurt can be solved by making sure the CCRM, cluster, engine harness, dash harness, body harness, and PCM are out of the same year of car. A lot of the rest is mix and match for free.





Boosted V6
It would be cheaper to swap in a ls engine and more bang for the buck. Hard to beat a motor that can support 700rwhp in stock form.


Active Member
And even harder to install said motor and then wire it so that everything, including the AC, gauge cluster, and anti-theft system still works. My car functions just like a stock 01 Cobra. Just because an LS is faster doesn't mean I'm willing to sacrifice the rest of the car.


Boosted V6
And even harder to install said motor and then wire it so that everything, including the AC, gauge cluster, and anti-theft system still works. My car functions just like a stock 01 Cobra. Just because an LS is faster doesn't mean I'm willing to sacrifice the rest of the car.

Nothing wrong with the dohc swap either.


Away from V6's for now........
It would be cheaper to swap in a ls engine and more bang for the buck. Hard to beat a motor that can support 700rwhp in stock form.

But then your stuck with a LS motor in your Mustang :facepalm:....... I guess its the thing to do these days....

700 wheel? So close to 800 fly in "stock form". I guess that depends on your definition of stock.


Away from V6's for now........
Whats heads and cam set up did you run on that?

My 427W is underway for my 90 LX..... going EFI though....


Away from V6's for now........
I just checked it out, hopefully the guy responds. If he does, I would be glad to point him in the right direction to get that thing making more steam; its under camed and has a tiny intake for that motor.

My GT is running great, I still think it needs a revised tune, but its ok for now. Took it to the track several weeks back, it ran spinning 13.7's at 104 mph..... I bet with stickies and a really good launch it would break into the 12's



Actually the heads are too small (AFR 205) - I should have used 220's or 225's. Trick flow stage 3 cam with 1.7 rockers. Intake is fine. Car pulls like a freight train - it does 11.7 in the quarter, and that ain't too shabby considering it's not setup as a drag car. We replaced the fuel pump and it stopped going lean at the top end. Haven't put it on the dyno yet after the fuel pump change, but we're guesstimating we gained the last 10hp we were missing. Carb is a quick fuel 850.


Away from V6's for now........
I also think the heads are on the small side, but not horribly.

Still stand by the intake and cam statements though. Super Vic intake at a minimum for something like that. 427W should have no problem making 500 wheel. I'm doing a 427W right now for my 90 LX with 240 TFS Highports, custom solid roller, probably gonna use shaft rockers, and I'm using the Victor/Glidden 2828 intake for it. Running a 4500 Accufab TB.

And I'm just making respectful observations, not trying to bash on your build. Bad ass car for sure.


I'm running a hydraulic cam, which limits rpm, and therefore HP and torque. A super vic intake is appropriate for drag racing, but that's not what I built my car for. In all actuality, I did it for the sound. The extra HP is a happy accident. :)

Phil II

Cone Destroyer
Uh, no. Hydraulic roller cams are very capable of high rpm. Your choice of lifters is probably the limiting factor.

Hydraulic flat rapper on the other hand...

Fwiw I'd leave it as is. I bet its got pretty good drive-ability and good response in the low and mid range.


Away from V6's for now........
I'm running a hydraulic cam, which limits rpm, and therefore HP and torque. A super vic intake is appropriate for drag racing :)

Well I respectfully disagree with both those statements...... However, if the car makes you happy as is, then thats all that matters.


Active Member
Moderators, can you move this to the Articles section? The information took a long time to compile, and the questions get raised over and over again and are answered incorrectly half of the time.