serious prob. after swtiching to standard

[Highoutput5.0]

i have a 95 mustang decent amount of mods. recently i switched it over to a manual trans. ive put the wiring harness pedals tranny and computer from the 94 doner car i also own into the 95. the problem is that as soon as i hooked up the manual harness to the gang connector underhood when i went to start the car it was running really rough, had trouble revving and was going very very rich out the tail pipes. the car could hardly also drive. when i changed nothing and left the manual computer in and just tried to see what would happen with the auto harness hooked up, but not hooked up ot any sensors or anthing else except for jumpin a couple of leads to start it, the car ran 1000 time better with just a little bit of rich condition. Any help would be appreciated. ive seen the swap done a few times and for most everyone else it was A ok.

mods for referance of confliction:
255lph fuel pump
FR Gt 40 cobra manifold
FR "F" cam
Underdrive pullys
Mac CAI
headders
H pipe no cats
flows
Fresh engine rebuild, its only been running for about 25miles still doing lots of other work to it bodywise and other little things
THANKS,
SAM

 

[vp6799]

Off subject for a bit. How do you like the F-cam??How is it idle wise??

I am in the process of doing the T5 trans swap from an auto and also going to install the F-cam.