This is a step by step guide for swapping a Mark VIII engine in your Mustang GT. This is a cheap, but labor intensive project. I give this as a high difficulty rating. You need to have a quality tool set, a lot of patience, and a good knowledge of mechanics. If you can change a head gasket, or rebuild a motor, you should be able to do this swap. If I have to tell you when to jack the car up, or explain how to remove the old engine, then this swap is not for you. The pictures are going to be in URL format for a clean post.
Parts that are absolutely needed:
97-98 Mark VIII engine, complete with vacuum lines.
97-98 Mark VIII Throttle Cable
97-98 Mark VIII Upper fuel lines. * These disconnect in the passenger side wheel well of the Lincoln.
93-98 Mark VIII thermostat housing
93-98 Mark VIII Alternator
96+ Mustang GT wiring harness.
96+ Mustang GT oil pan and pickup tube
96-01 Mustang Cobra Exhaust manifolds. * I prefer the 99+ because they don't have the air injection system that the 96-98 does.
96-? Mustang GT Coolant sensors.
96-01 Mustang Cobra water hoses.
* Manual transmission only parts
96-? Mustang GT 6 bolt flywheel
96-? Mustang GT clutch.
96-98 Mustang GT Pilot bearing.
Tools required:
2 floor jacks
2 Jackstands
A set of car ramps.
Multiple extensions and swivels
A decent socket set with at least one 8, 10, 13, 15, and 18MM socket
A decent set of wrenches with at least one 8, 10, 13, 15, and 18MM. And one 15/16th's wrench for the motor mount bolts. I recommend having at least two 10, 13, and 15MM wrenches.
A decent screwdriver set
A mustang Haynes manual.
Step 1. Remove the old 2V engine. This can be done in several ways, so pick your poison. I took mine out the top, leaving the transmission in the car. I deem this a mistake since I couldn't get the clearance required to reinstall the 4V engine and I had to remove the transmission and lower the K member to reinstall. You can leave the power steering pump and the A/C compressor in the engine bay and still hooked up as you will be reusing them on the new engine.
http://i108.photobucket.com/albums/n...d/SDC14321.jpg http://i108.photobucket.com/albums/n...d/SDC14327.jpg
Step 2. Locate a Mark VIII engine. I have heard that the Gen 1 93-96 motors will work, including the intake, but I can't confirm. I found a 97 engine, which has an intake more like the Cobra does and will work fine.
http://i108.photobucket.com/albums/n...SDC14337-1.jpg http://i108.photobucket.com/albums/n...SDC14338-1.jpg
Step 3. Remove the wiring harness from the 2V engine. Be SURE to take pictures of everything, so you can remember where everything goes.
http://i108.photobucket.com/albums/n...d/SDC14339.jpg
Step 4. Swap the oil pan and pickup tube from the 2V motor to the 4V motor. Also install the cobra manifolds and the motor mounts at this time. You can bolt the mounts to the K member, but I don't recommend it. It's a pain to get them attached once the motor is in and I had to grind the edge down to fit on the passenger side. The dipstick tube will have to be bent slightly to install the motor mount on the drivers side.
Step 5. Install the wiring harness on the 4V engine. Be sure to start with the fuel injector connectors and work from there. You will have to cut and splice several wires. These wires are the Idle air control, the EGR sensor, camshaft position sensor, and the two coolant sensor wires. * Note, the 4V engine uses knock sensors, the wire comes out from under the intake on the rear of the motor, I chose to stuff the wires under the intake. You will also have to thread the second coolant sensor from the GT in at this time.
Step 5B. Vacuum lines.
The mark VIII usues a vacuum brake booster, you will need to cap this line first, it's on the back of the engine and is the larger port back there. You can delete the line going to the air injection system. Run the PCV valve to one of the ports on top of the intake, then cap the other one. Take the EGR opening valve from the GT and run your hoses exactly like the GT would. The one coming over from the EVAP canister goes right under throttle body, there is a line under there.
Step 6. EGR and IMRC's. If you are keeping them both, read on, if you are deleting the EGR, but not the IMRC, skip to 6B.
Step 6 A: EGR.
If you are keeping it, you have a problem. The pipe that the Mark VIII uses is larger than the GT/Cobra uses, so it will attach to the EGR, but not the exhaust manifold. I took the GT pipe, on the manifold side and cut it in the straight section, then took the Mark VIII pipe and did the same. I then welded them together to make one pipe with the Mark VIII end attaching to the EGR and the GT end attaching to the exhaust manifold. You will have to relocate the IMRC motor and bracket to install the pipe.
Step 6 B IMRC's
You can get a delete plate, or you can keep them, or you can wire them open. Either way, you are going to have to remove or relocate the IMRC motor. I removed the motor from it's bracket, then cut the bracket in half, leaving the EGR sensor attached to the block. The IMRC motor can be relocated to the passenger valve cover.
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Step 7. If you are using a manual transmission, bolt your flywheel and clutch to the 4v engine now. Be sure to install a new pilot bearing on the 4v engine.
http://i108.photobucket.com/albums/n...d/SDC14637.jpg
Step 8. Prepare to install the motor in the body. Install the new throttle cable BEFORE installing the engine. * If you kept the EGR, you will have to cut a section of the strut brace on the firewall side, this is necessary to clear the EGR pipe.*
Installing the motor extremely tough to do with the K member and/or the transmission still in the car. It is IMPOSSIBLE to install this motor with the K member bolted in and the transmission still in the car. I had to unbolt the transmission and lower/slide it out of the way, then mount the engine on the K member. Then I had to set the car on the ramps, unbolt the K member and lift the body up enough to bolt the transmission to the engine. *I also believe that it will be near impossible to install the engine with the transmission bolted to it due to clearance issues, but I can not confirm this*
http://i108.photobucket.com/albums/n...d/SDC14644.jpg http://i108.photobucket.com/albums/n...d/SDC14645.jpg
Step 9. Remove the old fuel lines from their quick disconnects in the passenger fender well. Attach the Gen 2 lines to the fuel rails, then cut them off over by the old lines. Then attach a section of 5/16'ths fuel injector hose and clamp it tight to both lines on both ends.
http://i108.photobucket.com/albums/n...d/SDC14646.jpg
Step 10. Cooling system. You will have to bend the heater pipes on the motor out of the way of the heater core lines. I heated them up with a small torch and used a large punch inside the tube for leverage. It's tricky to get the radaitor hoses done correctly. You should get Cobra hoses, but you CAN do it with the GT stuff, but I am still unsure about the quality of this, so just get the cobra hoses.
Step by Step guide to installing a Mark VIII motor in a 96+ GT. 
lol
