96 Mustang Cobra starting and running problem

So i bought this car last October. 96 Mustang Cobra 5.0 Boss edition. Everything about this car has been modified. 87 Intake Manifold, some 96 Mustang parts, some 94-96 Ford Explorer parts. Since I've had it i've replaced the clutch kit, plugs and wires, distributor, alternator, charged the battery, battery terminals, fuel filter, and most recently the Idle Air Control valve. I've cleaned the MAF, IAT, and EGR valve the best i could with carbon cleaner. Now keep in mind when i bought it not all the sensors were plugged in and it ran fine but through trial and error with this recent starting, idling and running problem i have everything i can hooked up. Now i can't run the computer scan cause the connector underneath, near the front axle was never connected and must've dragged and is now melted. I'm pretty lost at this point..i'm thinking my problem is some sort of electrical issue. And i know nothing about electrical. On a cold start she'll start and idle fine for about 5mins. I've got the idle set for around 1500. She'll drop to around 800rpms and rough idle around 900-1100rpms. Test drove her the other day after i replaced the IAC drove great except for the squeeky clutch, went down a hill to a dead end went to put her in reverse, engaged the clutch and she died...when she did fully turn over i got her to move about 6ft and she died..finally after about 45mins of this...waitin and playin i got her back up the hill and on my street and she died again.. Finally got her in the drive way and I've been scratchin my head eversince..lost.. any knowledge or ideas will be happily accepted.. if you can please take ur time and include details.. I was never too car savvy till i bought this car.. now i've got no choice but to learn..

thanks,
Bizz