Lengthy post, but thanks for having a look…
I bought my first viper the other week, a 2000 Dodge Viper GTS with 16000 miles. It needs a few things, but at the top of the list is a MIL, P0355 – Ignition Coil E Primary/Secondary Circuit (Current). It is the only code. The car stars just fine, runs but seems like 2 cylinders are missing.
I don’t know much about the history of the car other than I am the fourth owner and there is about a 8 year gap between the second owner and third owner on the Carfax. The guy who had it before me kept it parked in a garage for a few months before I got it.

First thing I did was bench test the #5 coil, and yes, it was bad (resistance on terminals 2&3 came up as ‘open’). I replaced both coils with delphi coils, added Quality Wires, and champion RC12LYC plugs gapped to 0.035. I figured since the coil was bad, this would fix the problem and I figured it was time for new plugs anyways. To note, the spark plugs in cylinders 2 & 3 were fouled, all the others looked ok. This was not surprising since they are the cylinders associated with the fifth coil. I did have to shave the alignment tab on the 6-post coil so the connector would go on. I hooked the plug wires up as they were before, ignoring the numbers on the coil.
The code persists after changing everything out. There is no backfiring and the car still starts up normally. I traced the harness from the coil packs back to the PCM and did not find any breaks, and all the connectors seem to be fully seated. I reset the PCM by unhooking the battery terminals and zip tying them together and letting that sit overnight. After relearning the TPS, checked for codes (none) and then I restarted the vehicle and the code reappeared immediately. The battery was checked and voltage was normal, connectors are clean.

Just for fun, I placed an inline spark plug tester and found that cylinders 2 & 3 barely turn the tester on, all the other cylinders seem fine. I unplugged the #2 & 3 fuel injector harness from the injectors, started the car and there was no difference in how the car runs.
I am starting to suspect the PCM at this point, but I know this would be rare. I was suspicious of the triggering signal, which according to the service manual is the #4 wire, Green with a gray tracer. I unhooked the coil pack, opened up the connector and put a piece of wire in with the #4 pin to use as a way to hook a test light to it. Pin #4, which I was expecting to get no signal from, actually lit my test light up while the engine is running (I hooked one end of the test light to my jumper wire and the other end to ground). Then I hooked up my multimeter in the same manner and measured voltage with the engine running and I got what I believe to be expected: measurements all over the place and occasionally hitting 12.xx, the same as the yellow/violet wire.

Just for fun, I unhooked the coil, and unhooked the connector form the PCM. Resistance from each end of the harness is normal, and when I put 12.xx volts in one end, 12.xx comes out of the other.
I feel like this is probably a PCM issue but when I tested the green/gray wire with the car running, it made me doubt that. I am out of things to check and running out of things to read on the forums. I have a few other ideas, but I think I need some outside advice for some things to check before I have to acquiesce and pay someone to look over it.

Anyone have any advice or know what I can do to find a solution?

Thanks!