I'll try to keep this long story short.
1.5 years ago the trans died, recently replaced it. Replaced all fuel lines (with the vinyl lines), fuel filter, checked & cleaned plugs and boots, new alternator & belt, cleaned intake & exhaust manifolds w/new gaskets, plus a buncha other misc. stuff.

The car now starts and moves but the engine sputters at idle. The engine shakes every time it sputters. Engine throttles and sputter decreases at 3K rpm. Sound at exhaust can only be described as a low pitched "flub" with each engine shake. Heavy smell of what seems to be fuel.

I believe it is missing on one of the cylinders every so often as it is almost rhythmic. If that is correct or what is causing it I'm not sure. Also, i have no way of telling if the CEL is on as the bulb that acts as the CEL light is "missing". Most likely it was removed by the lot I bought the car from years ago.

It might possibly be a bad PCM but I want to leave that to a last resort because of the cost. I have access to a junk yard that has all the necessary parts if needed. I get them for next to nothing so any suggestions to replace other parts will be followed. Ant suggestions? Do places like Autozone and Advance Auto rent OBD II scanners and will that scanner help me? Thanks in advance.

Replace the coil cover (White thing) where the boots and coils plug into, get the CEL bulb working. Some auto parts stores will scan your car for free and try to sell you the sensors or parts that the scanner says must be changed.

Sounds good, I'll replace that. I'll grab the whole ignition module, coils n cover n try swapping them out. Is there a way to test the packs with a multi tester? Also, the car runs but not well enough to drive to have the codes read so I'll have to rent a tester. And, does anyone know what kind of bulb the CEL uses? It appears to have been soldered to the board, possibly an LED but I do not know the color, voltage..ect. I can grab a replacement from Radio Shack but need to know the stats on the bulb itself.

I read somewhere that each coil should have a resistence of 10,000 OHM to be OK.... CEL light uses a 194 Type bulb I believe, do a search on interior it be there for sure.