1988 Full-Size Bronco running rough

Ive been working on this truck for months now. It has been running rough like it has a miss. I have changed the plugs, wires, cap & rotor. It still idles rough but it smooths out and then rough again. The truck still has alot of power when you get on it it goes! I have changes the lower intake manifold gaskets, and the upper intake manifold gaskets. I had a Ford technician come and tell me it was two injectors on the left side of the engine so I moved them to the right side and still the same problem but the same problem, the problem didnt move with the injectors so thats cancelled out. I compression tested all the cylinders and all the readings are within specifications. Despite me being an experianced technician I took it to the Ford dealer to diagnose it and they said "we dont want your money take that thing out of here". I took the valve covers off and used a dial indicator on the lifters to see if the cam lobes were worn and they are all the same lift on each cylinder and each valve. The motor has 164,000 Miles and it is a 351 Fuel injected. I can not use a scanner and knock out the injectors because it is not sequential because it is an 88'. Any help would be appreciated this thing is turning into a flower pot in my driveway.

I remember something about 2 ign wires, perhaps #7 and #8 , (maybe others) that if they are routed next to each other , they will cause a misfire and possibly engine damage. Try rerouting the ign wires differently to prevent possible crossfire.

Did you check the Cat? Bad Backpressure does cause rough idling...how's your exhaust note?

Are you the long-term owner of this beast? Could someone have switched the engine on you?

Did you ever fix the problem??

I just had one more thought. I have seen Fords have a misfire caused by a leaking diode in the alternator causing a feedback to the pcm.but not causing a charging problem, seen it twice in 15 years.
Pull the plug off the alternator and run the engine to see if the miss disappears. If it does, reconnect to see if it comes back, repeat a few times to confirm. If that's the problem replace the alternator .
Let us know if you found the problem.

Does the computer give up any codes in the self test?