I think your going to have to provide allot more details as to what you did. Was not the 1996 351 a MAF Motor and the 1993 speed density ? Where's the MAF, what harness did you use, which processor. Did you time the motor ?
You did a basic swap, right up to the point that the 93-96 changes in fuel control, as to what parts you kept and what one's you left behind.
With something of this nature, you'd almost need a crystal ball to figure out what the problem is (if youre not present to watch what happened)
And no, the processors will be different, even if you where to put a 1993 351 where the 302 was different part number. I would expect it to run, just not have optimum power and fuel economy.
If you have the 1993 harness on the motor, and still a stick shift, you'd be looking for a F2TF-12A650-EB ECM
You might check out one of the Ford Gas Truck forums, those guys will probably get you dialed in quicker, than here.