Yes. One of the first things. I figured out the issue and finally got it running right today. Fixes are;
1) Pin out the engine management harness. Found numerous bad spots and overall roasted wires. Especially around the injectors. Found new/used harness that was 90% serviceable and tracked down each wire from start to finish replacing or replacing them as needed. I'm OCD that way. If the prints say yellow wire white tracer I found a suitable, matching color and replaced it. Solder every repair and heat shrink. Rewrapped entire harness in protective casing, reinstalled the harness.
This fixed the intermittent flashing check engine light.
2) Pinned out the PCM and found that I had no continuity between pin 17 (#3 injector) and pin 15 (ground). I tried this both without engine running and battery disconnected, without engine running and battery connected, and with engine running and battery connected. I had continuity with engine running but it didn't "pulse". It was constant which is not a good thing. I had continuity with engine not running and battery connected also but I thought that might be normal. SO, I broke down and pulled a PCM from the same year as mine, i.e. 2000, 4.0, 4x4, automatic and swapped it in. BAM!! Lol. Problem solved.
All I can say is if you come across this issue with a check engine light and misfire code be sure you check your engine harness BEFORE you replace the PCM. There's a good chance that if I'd just tried to replace the PCM it would've been ruined by the shorted out harness and I wouldn't have realise it. Therefore, troubleshooting and never finding the issue, because I'd have thought it couldn't be the PCM, it's already been replaced.
I'm going to open up the PCM and try to isolate the bad circuit shortly but I wanted to post my fix in case someone else has a similar situation. Thanks to everyone for their suggestions!:cheers::cheers: