Ok, well everyone that owns a v6 thinks about it. Very few attempt it. Even less do it successfully. Well i didnt take a whole lot of pictures when i did it since i did it alone. First off, i will say that you should get a complete parts car that runs. Otherwise you will probably nickle and dime yourself. I swapped a 5 speed to a 5 speed. Auto may be different and you should research more about it if you are going that route. I got a hell of a deal and scored an all out drag car with built engine, trans and rear. I will apologize for some of the pictures because i will borrow quite a few off good old google search
Tools:
Engine Hoist
Jack and 4 jack stands (or car lift)
good set of sockets and wrenches
nice to have impact wrench but i managed without.
breaker bar and/or cheater bar
pb blaster for stubborn bolts and nuts
Parts from donor car
Engine
Trans
clutch cable is different length
Rear End
Driveshaft
Intake
Exhaust manifold
Exhaust (now is the time to get true dual exhaust if you havent already)
Hydraboost system (v6 is too big and wont fit)
Brake/clutch pedal assembly
2 Brake lines for the hydraboost to the prop valve
radiator
radiator overflow tank
power steering lines that connect to the hydraboost
power steering pump
for a/c i believe you need new connections to the pump. I deleted the a/c so im not 100%
engine harness
ecu
gauge cluster
ccrm
the engine harness that goes from ecu to engine harness
Ignition switch with keys from the donor car unless you want to tow it to ford and get it reprogrammed
First off, if you dont know how to remove an engine you probably are over your head with this project. That being said, im not going to explain every detail on how to remove and reinstall stuff, but its easy to learn. This is the order i did stuff, you may do it in whatever order you deem necessarily. I would advise you to put labels on everything you disconnect and take lots of pictures to see how things are connected before taking anything apart.
Before:
Remove both engines, transmissions, and rear ends(I removed engine and trans together with all of the harness connected) I swapped rear ends prior to doing the actual engine swap which made it easier for me since i only have 4 jack stands. Before you remove the trans, first drain it into a jug and save the fluid. there are 2 plugs on the passenger side with 3/8" socket drive. drain from the bottom one. Fluids are expensive and you should try to save all of it you can. I put all new fluids in.
Remove driveshaft - 4 13mm bolts that connect to the rear end. put ebrake on to prevent the wheels from turning. Once unbolted the driveshaft will slide out. Fluid may come out so have something to catch it.
Next, while the car was engineless, remove the hydraboost system and brake pedal assembly from inside the car. swap these over to the "v6" and connect the lines before putting the engine in. I made the mistake of doing it after and boy that was a pain in the ass. The gt's is unbolted from the engine bay and the v6 is unbolted from under the dash. 4 bolts. and undo the hydraboost piston from the brake pedal
Next, remove the passenger fender. Underneath the fender you will find a little black box. This box is call the ccrm. same thing. You will need this and all the wires connected to it. First you must disconnect it from the ecu. The ecu is inside the car on the passenger kick panel. remove the kick panel and unplug the 3 plugs and unbolt the harness from the ecu. You will now be able to pull the harness out from the cabin. Replace everything including the ecu into the v6
Now, replace the guage cluster from the gt into the v6. It will have the correct speed and will not need retuned. Also, swap the ignition. To do this, there is a little hole on the bottom of the ignition switch. put a small scredriver or allen key in there while turning the key forward at the same time. The ignition will come right out. Reason behind this is because of PATS(passive anti theft system). Ill give a brief description of how PATS works. Key acts as a resistor, if the key matches the guage cluster, the cluster will send a signal to the ecu. If these match then the ecu will send a signal and start the fuel pump and start the car concurrently. If any of the 3 parts are not the same, the car will not start unless you turn PATS off. You dont have to get the ignition switch from the gt but if you dont you will have to take the car to a ford dealer and have them flash the computer and make new keys. Save yourself some money and just have an extra key on your keychain
Now is the time to put the engine and trans in. Like i said before, i installed them together. Once engine is in and bolted up. Reconnect all wires and hoses. Reinstal gt radiator with overflow tank. Reinstall power steering and connect hoses that go to hydraboost. If you have a/c reconnect that. I just used the fuel line from the v6 even though its longer. The throttle cable and cruise control cables are the same so just reattach those. Refill all fluids (coolant, power steering and whatever else you drained) Reinstall the gts driveshaft and refill the trans. Put exhaust back on.
Finally, if you were lucky and reconnected everything correctly, the car should start. I was super stoked when i tried and it did start on the first try. This is what it should look like when reinstalled.
I will say this may not be everything since its been a couple months since i did it. If anyone has ANY questions about the swap, ask me or send me a pm. Sorry for the lack of pictures. I did this swap by myself and never grabbed the camera
Tools:
Engine Hoist
Jack and 4 jack stands (or car lift)
good set of sockets and wrenches
nice to have impact wrench but i managed without.
breaker bar and/or cheater bar
pb blaster for stubborn bolts and nuts
Parts from donor car
Engine
Trans
clutch cable is different length
Rear End
Driveshaft
Intake
Exhaust manifold
Exhaust (now is the time to get true dual exhaust if you havent already)
Hydraboost system (v6 is too big and wont fit)
Brake/clutch pedal assembly
2 Brake lines for the hydraboost to the prop valve
radiator
radiator overflow tank
power steering lines that connect to the hydraboost
power steering pump
for a/c i believe you need new connections to the pump. I deleted the a/c so im not 100%
engine harness
ecu
gauge cluster
ccrm
the engine harness that goes from ecu to engine harness
Ignition switch with keys from the donor car unless you want to tow it to ford and get it reprogrammed
First off, if you dont know how to remove an engine you probably are over your head with this project. That being said, im not going to explain every detail on how to remove and reinstall stuff, but its easy to learn. This is the order i did stuff, you may do it in whatever order you deem necessarily. I would advise you to put labels on everything you disconnect and take lots of pictures to see how things are connected before taking anything apart.
Before:

Remove both engines, transmissions, and rear ends(I removed engine and trans together with all of the harness connected) I swapped rear ends prior to doing the actual engine swap which made it easier for me since i only have 4 jack stands. Before you remove the trans, first drain it into a jug and save the fluid. there are 2 plugs on the passenger side with 3/8" socket drive. drain from the bottom one. Fluids are expensive and you should try to save all of it you can. I put all new fluids in.
Remove driveshaft - 4 13mm bolts that connect to the rear end. put ebrake on to prevent the wheels from turning. Once unbolted the driveshaft will slide out. Fluid may come out so have something to catch it.

Next, while the car was engineless, remove the hydraboost system and brake pedal assembly from inside the car. swap these over to the "v6" and connect the lines before putting the engine in. I made the mistake of doing it after and boy that was a pain in the ass. The gt's is unbolted from the engine bay and the v6 is unbolted from under the dash. 4 bolts. and undo the hydraboost piston from the brake pedal

Next, remove the passenger fender. Underneath the fender you will find a little black box. This box is call the ccrm. same thing. You will need this and all the wires connected to it. First you must disconnect it from the ecu. The ecu is inside the car on the passenger kick panel. remove the kick panel and unplug the 3 plugs and unbolt the harness from the ecu. You will now be able to pull the harness out from the cabin. Replace everything including the ecu into the v6

Now, replace the guage cluster from the gt into the v6. It will have the correct speed and will not need retuned. Also, swap the ignition. To do this, there is a little hole on the bottom of the ignition switch. put a small scredriver or allen key in there while turning the key forward at the same time. The ignition will come right out. Reason behind this is because of PATS(passive anti theft system). Ill give a brief description of how PATS works. Key acts as a resistor, if the key matches the guage cluster, the cluster will send a signal to the ecu. If these match then the ecu will send a signal and start the fuel pump and start the car concurrently. If any of the 3 parts are not the same, the car will not start unless you turn PATS off. You dont have to get the ignition switch from the gt but if you dont you will have to take the car to a ford dealer and have them flash the computer and make new keys. Save yourself some money and just have an extra key on your keychain
Now is the time to put the engine and trans in. Like i said before, i installed them together. Once engine is in and bolted up. Reconnect all wires and hoses. Reinstal gt radiator with overflow tank. Reinstall power steering and connect hoses that go to hydraboost. If you have a/c reconnect that. I just used the fuel line from the v6 even though its longer. The throttle cable and cruise control cables are the same so just reattach those. Refill all fluids (coolant, power steering and whatever else you drained) Reinstall the gts driveshaft and refill the trans. Put exhaust back on.
Finally, if you were lucky and reconnected everything correctly, the car should start. I was super stoked when i tried and it did start on the first try. This is what it should look like when reinstalled.

I will say this may not be everything since its been a couple months since i did it. If anyone has ANY questions about the swap, ask me or send me a pm. Sorry for the lack of pictures. I did this swap by myself and never grabbed the camera