Poor spark from coil on 2 cylinders

I have a 1986 6 cyl, 3.0 liter Grand AM that was running fine and all of a sudden started running poorly and rough. I replaced the EGR valve since it was leaking, all the vacuum hoses that were cracking and the PCV valve since it was original. It started running better but was still rough, so I changed the spark plugs out and the wiring since it was original wiring, but it still ran rough. I pulled the plugs off the coil one at a time to isolate if it was one of the cylinders not firing properly and found that all but two of the ports on the coil (3 and 6) would throw a 3 inch arch to the mounting screws. I tried replacing the coil thinking the coil was bad, but it made no difference. If you put a plug in the wires of cylinders 3 and 6 (3 and 6 are in the same partition of the coil), then ground it to the block it barely sparks. Could there be a problem in the circuit board in the mounting base under the coil? I'm just not getting the proper voltage output to the coil tower points.

Sounds like you nailed that one. The circuit board you are looking at is the control module, they are fairly inexpensive and easy to replace.

Thank you, I will look into getting one for replacement.

I took the control module off and carried it to AutoZone, they tested it and it failed as suspected. A new module fixed the problem, unfortunately it was a little over $100, but at least the problem is fixed. Thanks for the confirmation on the diagnosis.