I'm going through this now on my 98 GT. Engine is a 2004 Explorer 4.6, 21,000 miles, paid $1200 for it.
1. The timing cover is different. It's missing the boss to mount your power steering pump. It also has a bolt hole in a different location than any mustang cover. It's to the right of the water pump, I'm using a F6AE cover and using it as a guide to drill into the block 3/8" and install a heli-coil and put a stud there.
2. The oil pan is different. And the oil pump pick up. I drilled through the spot welds from the Explorer oil pan and took the crank scrapers out, and welded them into a FRPP mustang pan. Also swapped out the oil pump & pick up for the FRPP Cobra model, installed the windage tray also.
3. Even though the intake manifold is a PI version, there is no provision to extract water out of the rear passenger side head like on a Mustang. Bought a new one from Kar Kraft. The thermostat cover is pointing the wrong way.
4. You need a Mustang heater tube. The Exploder has an extra tube coming off of it.
5. Oil filter adapter is totally wrong. Using my old one.
6. Valve covers must be changed for my old ones.
7. Exhaust manifolds are different.
8. Still need to see if the Exploder water pump is the same as my year model (long or short).
Not as easy as people make it out to be!