Eric, you were correct the first time. The 94/95 ECU does not perform as well as the 93 which is considered the optimum for the 302 by most as far as stock computers are concerned.
If you are going to pull an engine, try to follow the harness(s) from the two 10 pin round connectors back to the computer and to the next set of connectors (as much as possible). Also get the O2 sensor harness: Ford has obsoleted these, but Painless now has them, so it isn't as big an issue as it used to be. I used a combination of a Chiltons, the Ford EEC-IV book and the painless wiring guide to marry the chassis harness into the computer harness. Oh yeah, I also had the book that came with the computer harness I bought from Ford. There was only one error in the wiring diagrams in the Chiltons and it involved the WOT shut off of the A/C and wasn't too hard to figure out.
The 94 intake worked fine for me. Keep in mind that I use the Porsche transaxle which allows my motor two be, at least, a couple of inches lower than with the Audi/Getrag or Renault transaxles. If the 94 throttle body came straight out of the middle of the plenum (like the 89-93) it would have been easier. But, a short 3" 45 into a ProM MAF and then a ~5" radius 3.5" 90 put my K&N right in front of the door scoop on the passenger side of the car. The rear clip opens and closes with no problem for me. Also keep in mind that there are different configurations of that area. I'll try to get a photo of the intake/plenum posted for you.
[ January 28, 2003: Message edited by: Lynn Larsen ]