RPMs drop then engine shuts off

This is what I have:

96 mustang gt body/computer
02 gt engine
03 gt tranny
flowmasters
no cats/no resignators
3.55's

My problem has something to do with the old computer:
When engine breaking in 4th or 5th, not much.. maybe letting it break from 3.5k to 2k, and then push the clutch in, it idles all the way down and the engine cuts off. If I let it idle in neutral, the rpms will drop, then come back up, then drop again, then come back up.My friends dad owns a ford dealership and his guys set my 'low idle' around 700rpm and said it should fix it, but it didnt. He said it had something to do with the computer thinking it was about to die and started dropping rpms, realized it was ok and the rpms came back up..I just ordered some MIL Eliminators because i have CE light on for the o2 sensors. Will the mil eliminator help with this problem? or why didnt the ford tune last? I'm also installing a speedcal today, i doubt it has anything to do with the rpms though.

Please help.