Ok, update..
ECU came back from the testing place, it is not the problem. I removed the Quarterhorse from the ECU when I sent it out and left it off when I reinstalled the ECU. I am now NOT getting a huge list of codes I was before.
I ended up throwing a P0308 code. I pulled the COP units and plugs out to check them. Everything looked ok. I swapped COP 8 and COP 5. I again had a misfire warning. I plugged in my mongoose cable and checked for any hiden codes. I didn't see any but I checked the TIDs and I am failing these ones:
Phase 2 0.020 cruise leak check vacuum bleed-up and max leak threshold
Phase 4 Vapor generation max change in pressure and max threshold
Phase 4 Vapor generation max absolute pressure rise and max threshold
Cylinder 05 misfire rate and catalyst damage threshold
Highest catalyst-damage misfire and catalyst damage threshold misfire rate
Highest emission-threshold misfire and emission threshold misfire rate
Obviously the COP unit was bad. I will be replacing that. What about those Phase 2/Phase 4 TID failures ?
Finally got my COP unit in the mail today. Jackasses didn't tell me they were going to mail it from the other side of the damn country so it took a week to get here.
Put the COP in and cleared the codes. The car hasn't run this well in forever.....
I feel dumb as apparently the quarterhorse was the cause of all ther weirdass basket o codes I was getting.
I am still failing some TIDs but I'll post a new thread for that as at this point it is way beyond the scope of the OP.
To everyone that said I should pull the quarterhorse unit off and see what happens, you guys were right and I feel dumb.