Here ya go....
Alright so here goes. This is all MY personal experience and if I leave anything out, I am sorry. I will probably be editing this post for a while.

Now everything I am stating here has to do with a 99 GT going to a 4V complete swap. Other years might have other little differences. For example, 03/04 Mach 1s have a different from timing cover from a 99 Cobra. They changed the tensioner setup and some of the A/C lines. Therefore if I go to Ford and get a brand new Mach 1 timing cover, I will need other swap parts for a Mach 1 and not a 99 GT. It could make the swap rather expensive. Also another note, all the ‘Ford’ parts I got from Randy on - Ford Mustang Performance from Modular Depot he sells Ford parts straight to the ModDepot community for really competitive prices even with shipping. So keep that in mind when going to your local Ford dealer and finding out I got my Ford Parts way cheaper. I will give you guys LIST prices and depending on where you get your parts it could be cheaper…so this is NOT what I paid for this stuff. Alright…on to the parts

First off if you plan on doing this on a budget, get a complete 32V motor from a wrecked 99/01 Cobra, 03/04 Mach 1 or 03-up Lincoln Aviator. I chose the latter of the three, there is a parts website called Welcome to Greenleaf and they usually have these motors complete in the $2500-$3000 shipped range. I got mine used with 2,000 miles on it, shipped to my door for 2000 bucks. Also the motor was complete from Throttle Body to Oil pan.
Now there are a lot of Performance shops out there that could use the Aviator intake for performance gains. The Aviator uses a dual runner technology. Air has two paths to take when using this intake. It has butterflies in it that allow more TQ at lower RPMs and more HP at high RPMs when the butterflies open. It is controlled via the computer of the Aviator SUV, but you can rig this up to work with a window switch, similar to what you do with turning nitrous on and off.
There are other problems with the Aviator intake as well. It is really, really TALL! So tall that some can’t even fit a 2.5" cowl hood on it, some have, but it comes really close. Most go with a 4" cowl hood. I am telling you, the Aviator intake is HUGE in comparison to the Cobra/Mach intake. I choose to sell this intake, I threw it on eBay for 300 buy it now and it sold in 8 hours. So take that off the top of 2000(or whatever you got your motor for) and you have a complete low mileage 4V motor for 1700 or so.

If you are not on a budget, FRPP also sells the Mach 1 motor and harness for $6,000, brand new in the crate. Is it a good deal, while some would say yes, some other would say no. It is a good deal because it comes with EVERYTHING you need, intake to oil pan, wiring harness to headers. The only thing is, if you put this motor in a 99(maybe 01) you might have to swap some Mach 1 things into. Like I mentioned above, A/C lines etc, etc.

So you have your complete motor now, one way or another, how do I go about tracking down everything I need. The Aviator timing cover will work with the Mustang, but there are some differences you need to be aware of. First the P/S pump sits up in the bay a little higher than the Mustang 4V cover. Some have used the Aviator cover, but some say it causes header and other alignment issues.
I chose to use a 99 Cobra timing cover. All the lines are the same on the 99 Cobra to my 99 GT and it was a direct swap. So my suggestion to you is get a 4V timing cover of the year of your car. If you have a 00/02 GT, look at getting a 01 Cobra cover. Do some research, ask buddies to look at his 01 Cobra or Mach 1 to help. Like I said, ALL my knowledge is from doing is on a 99 GT. This 99 4V timing cover ran me 100 bucks. I checked from Ford and new, this 99 SVT cover was 265 bucks. So I made out pretty good. I cleaned it up and painted it and it looks and does its job like new.

Also inside the timing components are different. The fixed guides and swinging guides are different although the chains and lower gears are the same, along with the upper PRIMARY timing gears. The guides are different, but my buddy and I just did a 4V swap on his 2V and we wanted to use his forged bottom end for the 4V swap, so we dug into the swap way more on his than on mine. Now with the guides being different we did not have the full 4V timing chain setup like I did with my Aviator swap. What you NEED are the fixed guides as they are different, but the 2V ‘swing’ arms will work. Are they exactly the same, NO, but we have them on his car right now and they seem to be doing fine. Now something the 4V has that the 2V doesn’t is two more cams, which means twice as many parts under the timing cover. There are two secondary gears per side (4 total) along with a smaller secondary chain with secondary tensioners for each side (2 total, right and left) This little stuff is expensive, this is why a complete motor comes in handy or even finding them used somewhere. Parts stores don’t carry 99% of this. Trust me, we checked.

Now with MOST of everything under the timing cover and timing cover itself taking care of. What do we do about all the ‘external’ parts? Well let’s tackle it from the top of the motor to the bottom, assuming you have an Aviator motor. First to go is the Aviator intake, so now you need a Mach 1 or Cobra intake and parts. I got my hands on a ported/extrude honed 01 Cobra intake with T/B for 700 bucks. Most stock Cobra/Mach 1 intakes go for about 350-550 depending on what is on them already. Also you can re-use the Aviator gaskets so you don’t have to buy new ones. They are the same.

Also if you get the Cobra intake you also need some swap parts as well that will nickel and dime you. First off the Aviator uses the same 4V Alternator as the Cobras and Machs. So that will save you some cash, but the bracket that bolts to the alternator and intake is different from the Aviator to the Cobra. The Aviator uses a ‘stepped up’ bracket and the Cobra is a flat even bracket. Do you HAVE to get the Cobra bracket…No. I straightened my Aviator bracket out and drilled a new hole and it works just fine. If you want it to look perfect, buy the Cobra/Mach 1 bracket. I think it is 14-15 bucks from Ford.

Also on the Alternator side, the 2V harness is different than the 4V. Get a Harness repair kit from Ford, P/N 1U2Z-14S411-UA, list is $25.38. As far as cutting and splicing it in, it really isn’t that hard. Just remember that the 4V Alternator is wired 180* out from the 2V. There should be a green and yellow wire. Switch those around and you are good to go. The middle wire is still not used, pull it from your new connector and discard it. If you do not switch those wires around, you will get a ‘batt’ light from the Alt not charging. If you get this, this is most likely your problem.

So the intake situation is figured out, but what about fuel rails. 99+ Mustangs/Cobras use a returnless type fuel system. So any rail from a 99+ 4V Cobra or Mach 1 will work. Even the 03/04 Cobras use the same rail as the latter years. Also the fuel injectors from the Aviator are the EV6 style like the Cobras and Mach 1s. If you have EV1 style injectors you have one of two options. You can splice in the EV6 harness and use the injectors that come on the motor or use EV1 injectors. I didn’t really feel like cutting the injector harness so I got a set of FRPP 30lb/hr injectors on eBay for 120 bucks shipped. Problem solved. Also on the intake side is you need an inlet tube (air intake). I was holding out for a cheapo stock one, but I couldn’t find one for what I wanted, so I sacked up and bought a 03/04 Mach 1 inlet system from K&N on eBay for 220 shipped.

Now on the inlet system, as for me, I have a separate IAT(Intake Air Temperature) sensor, and the Mach 1 inlet does not. The Mach 1s have the IAT integrated into their MAF. I had to drill a hole in it and plug it in. Not a big deal, but something you can’t over look. And just don’t hang it in the fender well. That is NOT the correct way to run/tune your car, I don’t care what ANYONE or shop says. I have data logged my car and even N/A the inlet air temps are different than ambient air. Another option is you could get a 03/04 Mach 1 MAF and use that as you MAF and IAT. You just have to de-pin your IAT and stick it into the outside 2 pins of the MAF connector. More on that if questions arise and I will provide pictures if needed.

Alright so the intake portion is taken care of, what about the exhaust? 2V Mustang headers are physically the same. The 2V uses a round port design as the 4V mustangs use an oval port design on the flange…and there are even 2 styles of oval design. 99/01 Cobras use a TRUE oval design and the 03/04 Cobras, Mach 1s and Aviators all use a ‘square’ oval port design. Will any header work with either? Yes, but there will be a LITTLE and I mean LITTLE port match difference. You can use stock any Cobra or Mach 1 manifolds on either style head and it will work and will bolt up to your stock 2V exhaust the same. The only difference in the exhaust from Cobras and GTs/Machs is the Cobras use IRS so the cat back is different, and the headers use oval port designs, other than that, all the other exhaust bolts up in the same locations. So take stock Mach headers, and bolt them up to your stock GT exhaust…no adapters needed. You will however need a new passenger manifold collector gasket (about 7-10 bucks from Ford)
I chose to get 99-up BBK longtube headers and matching O/R h-pipe. Now if you have emissions in your state, you might want to consider keeping stock manifolds and all the emission equipment. I stated earlier that the ports are different from 99 Cobras to 03/04 Cobras, Machs and Aviators, but I still got headers for 99/01 Cobras. BBK doesn’t make a 03/04 specific flange, but it does work. I have them on my car and they have VERY, VERY minimal port mismatch. I have seen other headers that have horrible port mismatch, but from my experience the BBKs aren’t noticeable and I doubt I am losing any power from it. The only other companies I know of that make specific 03/04 headers are SLP and Kooks. Look to spend about 1000 bucks for just the headers. I got my headers and H-pipe for $525 shipped. These are the ceramic coated ones. I believe a vendor on SVTPerformance.com is still selling these for this GREAT price! That is where I got mine. Also if you get Longtube headers you need to get some O2 extension harnesses. I also got these from BBK. I think I paid something like 35 bucks.

Next up is the oil pan. The Aviator oil pan is deeper and will not fit the Mustang platform, just take the oil pan from your GT and slap it on the 4V motor. The only thing you will need is a Cobra oil pick up tube. I had one lying around so I used that. You can’t use your 2V pickup as the tube is bigger from the 4V to the 2V. Also re-use your 2V dipstick tube. The Aviator one will work, but I think it is too long and will hit the hood.

The motor is pretty much ready to go in, once you get it in you will need to do some other things to make it all work. First is if you have an Aviator motor and valve covers, they use a tall oil fill, you need to ‘unscrew’ that to make it clear the hood, and put the oil cap back in the valve cover.

Also the Cobra Throttle and Cruise cables are different. So you also need to source out those from Ford as well.
Throttle Cable 1R3Z-9A758-CA $50.66
Cruise Cable XR3Z-9A825-BA $27.98

Also before you drop the motor in, you better realize that your 99/00 GTs came with a 8 bolt crank, and the Aviator motor you just bought has a 6 bolt crank. Just make sure you get the right flywheel for what you have. Here is some general info on Flywheels and years of cars they come on…

96-98 GTs use a 6 bolt 10.5" flywheel for 10.5" clutches
99-00 GTs use an 8 bolt 10.5" flywheel for 10.5" clutches
01-04 GTs use a 6 bolt 11" flywheel for 11" clutches

I already ordered a FRPP HD King Cobra Clutch in 10.5, so I contacted my buddy with a 96 GT flywheel for sale and got it for free, surfaced it and it has been working great. Remember no matter what bolt pattern you have, just make sure you get the clutch for your flywheel. Any 10.5 or 11" clutch will fit in either the T-45 or T-3650 transmission, so don’t worry about fitment into the transmission. If you have an automatic, I can’t help you there, but I am pretty sure as long as you have the correct bolt pattern flexplate for you converter, you should be fine.

Belt routing is the same from the 2V to the 4V as long as you use the correct year timing cover for your year. Obviously if you have a 99 GT and you use a 03/04 Mach 1 cover, the belt routing will be that of a 03/04 Mach 1 and NOT your 99 GT.

Alright now that we have the motor in the car and everything looks to be going good, this is the sucky/tedious part. Wiring up the COPs(Coil on Plugs). *Sigh* this sucked. On the 2V, the COPs sit right next to the wiring loom and only have about 2-3 inches of slack out of the main loom to the COP. On the 4V, the COPs sit under a cover in the middle of the head and the wire comes out of the loom in the back and feeds under the coil cover and runs to each COP in the middle. Also the COPs for the 4V are different from the 2V. I got my 4V COPs and wiring for 80 bucks shipped. Look to find these used, they run about 40-60 bucks EACH new and will make your swap rather expensive.
So tear all your wire loom off the main harness coming down the side of your intake where the fuel injectors sit. You will see a common color wire on all the COPs and a unique color wire for each one. Cool thing is, Ford made the unique color wires the same from 2V to 4V. So if number 5 is pink on the 2V, number 5 on the 4V is pink, so you don’t have to worry about mixing up the wires and firing order. What I did was write down on paper what color was what cyl and made sure I put it back that way.
What else can I say about doing this, pull the wire as far back as you can, splice in the wire and wire up the COPs. Now, Ford did do something to make this tricky as well…the 2V connectors will work, but they don’t ‘clip or hold’ as well as the 4V connectors. Either way you go with the connectors, you need to make note of the polarity. The 2V COPs have 180* polarity switch that of the 4V. Just another thing for Ford to make the 4V a little different than the 2V. If you look on your 2V COP you will see a ‘B+’ on the receptacle, if you look on the 4V COP, the B+ is on the other side. Just make sure you don’t wire these backwards or you will fry the computer or the COPs. The B+ is for the common color wire which was yellow/white on my car. This is the power wire that has a +12V on it when you turn the key on. The other wire is your control side that when the computer wants a spark it sends the signal to the COP to release the Voltage into the plug(s) to spark it. So after you realize how the system works, I doubt you will have any problems wiring it up. Just make sure you have enough wire to do it.

This next part will kill you. All the coolant parts and what not are COMPLETELY different from 2V to 4V. There are 5 separate hoses, and a thermostat housing that are all needed and you can only get 1-2 of these hoses at a local parts store and the $$$ savings isn’t worth it as the hoses aren’t perfect like the Ford ones are. You also need the expensive coolant crossover tubes. Here are some part numbers all QTY are 1 unless noted…

Coolant Crossover- XR3Z-8548-AD $135.91
Radiator Hose- F7ZZ-8260-AA $21.96
Radiator Hose- F6ZZ-8286-C $11.33
Hose- F7ZZ-8A593-AB $29.07
Hose- F7ZZ-8K576-AC $25.31
Hose asy- F8ZZ-8C350-AA $17.83
½ Thermo housing XR3Z-8K528-AA $58.80
½ Thermo housing F6ZZ-8592-BB $37.74
Seal for T-stat F1VY-8255-A $7.98
Bolts for T-stat -W500015-S309 $2.20 x 2

All this little stuff adds up, trust me. Just this one order I spent 340 bucks on it. Could you get it cheaper on eBay used? Most likely, but I didn’t have time and I didn’t want to piece it together, so I got it all new and knew it worked. Also the Coolant Temp Sensor is located on the passenger side of the 2Vs and the 4V it is in the coolant crossover on the bottom driver side. Easiest way to do this is splice in some wire enough for it to reach. I ordered a NEW connector kit from Ford as my tab was broke so I just used that and the wire that came on the connector was plenty long enough.

Another thing to note about the cooling system is the 2V uses a different tube under the intake in the valley. So you need that (I can’t decipher which one it is on my invoice, but if you call Ford they will know, just order one for a 99/01 Cobra or 03/04 Mach 1) Also on the 2V the heater core got its coolant from the intake into the heater core then out of the heater core to under the intake. The second part of that hasn’t changed, but the first has. You no longer have a PI intake and the intake fore the 4V doesn’t have provisions for that. Cobras and Machs have a tube on the back of the head that take the heater core the coolant and then sends it back to the water pump. If you do that, you need the ‘crack pipe’ (that is what it looks like on the back of the head) and the hose from the pipe to the heater core. I did a complete ‘cooling’ mod on my 4V swap so if you want more information on that, I can do that later in the write up.

Also another thing on the coolant side of things, the oil filter/coolant hose adapter for the 2V and 4V are different, but still hook up the same. Meaning the 2V one will work without ANY modifications, but the stock 4V adapters have a ‘oil’ cooler integrated into it, so do you need that? The Answer is No, I have my stock 2V one on there and it seems to be working fine. If you do want the oil cooler, look to spend about $100-200 for it.

Well I think I hit about everything needed. I am sure you will all have questions, so post away and I will do my best to answer all questions. Thanks

Matt