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 ?