5.0 Missing Under Load When Hot

I'm a little stumped with this one. I have a 1990 foxbody with a 306 H/C/I. The car ran fine until i swapped the T5 out for a TKO 600. Now it is missing pretty bad at low RPM (<3500) under a load but only when it is hot. I assume it has to do with the way the car determines the air/fuel ratio in closed loop, but when I unplug the MAF it idles like crap and runs a little rough, but the miss mostly goes away when I accelerate under a load.

I have done the following:
- Replaced O2 sensors
- Replaced Plugs
- Replaced Plug wires
- Cleaned the MAF (with actual MAF cleaner)

It has an almost new cap/rotor, coil, MSD box, fuel pump, and the injectors/MAF sensor are not too old either. I am just trying to figure out what could have happened during the tranny swap. I looked at the vacuum lines along the intake and did not see/hear anything obvious. It will buck/skip/sputter pretty bad under acceleration in any gear less than 3000RPM..if I give it gas past 3000RPM, the miss/sputter will go away and the car will pull and run great. I've done web searches and can't seem to pin point a common problem. Any help is greatly appreciated. Thanks guys

I suspect it could be the TFI module. I have been down that road before when using an old unit off a parts car. But I had always remembered TFI modules as either working or not working. And this is a low speed/low RPM miss. The diagrams are awesome though, I will definitely run an Ohm meter on it when I get home and see what it says.