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I saw there were 5 threads that were asking this same problem. Every single one suggested it was a ground, but that didn't make sense to me, and none of those were ever answered.
I found a new local mechanic, (and I think he's on the forums somewhere), but we both thought with all of that happening at once, the only thing they all share in common is a CL 2 Serial data.
I went back over what I did, and found the problem. When I originally pulled the aluminum covers off the PCM connectors, I pinched one of the wires putting em back on. The covering wasn't broken, but upon detailed inspection I could see it was "smashed", and without cutting it open, I must have cut the thin (what is that 22g) wire. I cut out and replaced the wire, and was able to immediately read with my code reader, and reset codes. All the issues I was having are all gone. Checking my pinout, that wire is a CL 2 serial data.
Perhaps I'll post up the schematics for the CL 2 serial data connections that go into just about every electrical connector under the hood and dash, but you're probably better off buying the PDF service manual, or going back over what you last did. If anyone comes across this searching, my first suggestion would be to go back over the wires at the connector for the PCM. They are incredibly thin and delicate. If you kinked one you may have broken the few threads inside.
Thanks for the update. Had not though about having the harness cover off to add Efans. The wires are tight as mentioned and can be damaged easily if not carefull enough.
If you are like me, this is probably a problem you caused. As I said earlier, those wires are incredibly thin, and if you messed with/crimped/folded/bent/PINCHED those thin wires, you may have broken the strands inside the casing and might never even see it. Since nobody else added anything to this topic in any thread I found, I will at least add this:
And if you have a several thousand dollar + scanner, (the aultel one that does modules is $4k+) it would scan the modules and give you these codes, (which don't help you without it, and it would tell you this if it could).
If you are not sure where the connectors are:
That's all the help I can provide on this issue. Good luck.