Thought I had this problem licked, I was wrong. Here's the background:
Snapped a crank in 85GT 4 spd 2.8 in Dec, installed a rebuilt motor. Car ran fine prior to snapping the crank(actually still ran after if you can believe that!) I had an occasional EGR code but that had been like that for ages, I assumed a faulty EGR sol.
Anyway I did have some issues with the fuel pump relay just before I swapped motors. I could tell the car was running the pump from the oil press sender. WhenI swapped the motor I spliced in the relay harness frommy parts car as the one in my car was badly corroded. I am not sure if this is related or not.

I did not get a proper 2-4 sec pulse to the fuel pump from the ECM and I checked all wiring right back to the ECM, no pulse. I assumed a bad ECM and swapped the one from the parts car. That worked breifly then also stopped so it seems both ECM's are fried in the fuel pump circuit. I have run the car since then with a jumper on the relay and just removing the fuse when stopped. I had planned to address that now that its warm. I did at one point have a wire attached wrong on the relay circuit(I think this is key to my problems) I fixed that. All wiring on the car seems normal and I did add another ground to the block

Ok my current problem is rough idle and stumbling on acceleration. I have changed IG mod, cap/rotor, wires are fine. I do notice when I checked timing that #4 cylinder misfires quite regularly. its the only plug wire that seems to do this and yes I swapped wires to see if it was a bad wire.
Is it possible the ECM is actually malfunctioning and misfiring only one cylinder? The car runs pretty decent and is reliable, just stumbles when i accelerate. I am pretty much sure this is a timing/ignition problem as fuel system seems fine and I can see this stumble on the tach. I have tried both ecm's and they both do it. I did try disconnecting the tach filter and initially thought it was better but was wrong.
I am going to look for another ECM but am hesitant to try that not knowing if it will help or if for somereason it will fry that one as well. I can't imagine the ECM is semi fried and the car still runs not bad, I guess it is possible tho.
Im running out of ideas on this one.
Idea's?
TIA

It might be your cap, you replace that? Perhaps under the cap its a little corroded for #4.

Not exactly sure on how to check something like that(prolly way off on this and I'm sure there is a better way but just off the top o my head). Maybe pull the wire off plug and leave it on intake, have someone start the car and look at the sparks.

Then if ya notice its missing(perhaps theres some sort o checker that just plugs on and checks voltage etc) then pull the one end off the cap and just switch it to another cylinder and see if the sparks are more constant(don't plug other end back on plug).

Dunno might be a fools way o checking... I am no mechanic.

Seems a little worse today, car has stalled at idle a number of times and its running rough at idle.
I swapped plugs last nite, they didn't look as tan as i'd like but they didn't look extreme by any means, maybe a bit black but that could be from the extreme rich I had when I first started the new motor(broken vac line). As I said right now the car sorta runs ok, just doesn't have the acceleration response thats normal. You can feel it missing when you depress the pedal. Running at moderate speed with low rpms in 4rth is "jerky".
I will try fuel filter tomorrow nite and I think I have another coil lying around which I am gonna try too. I was playing with the timing light again last nite and it may not be just one cylinder, but it doesn't appear to be many at once. I have an exhaust leak on the front bank so I will redo the gasket on that as well but this seems totally like an ignition problem. I found a used ECM for $75 so I may pick that up later this week too. The fuel pump prime circuit isn;t working anyway.

The cap and rotor were new when i swapped the motor and I tried another new one last week. TPS seems fine and its not throwing any weird code. God I hate s#$t like this, very frustrating!

Keep the suggestions coming...