Moozery, when I got the car it had sat for awhile so I also did a vigorous coolant flush. Had the nasty Dexcool sludge. I used the flush GM recommended and left it in for a few days. Then I rinsed with a ton of water until it came out mostly clear. Also, I've replaced the HGs and intakes so I know it was at least decently clean inside the water passages. I put green in.

Green97, I have not done a CASE relearn because I am using the ECU that came with it. Not sure if it would help, but I don't want to pay the dealer for it. I have another ECU from the same module year and features, the engine runs the exact same with it in as well. Same misfire pattern.

Fst, I've only half assed checked for a vacuum leak by going around the engine quickly with a small propane torch. I have replaced all gaskets and seals when I redid the heads up and it had no effect, so I have kind of ruled this out. I don't have a good place to make/use a smoker, but it is something I am considering when I have the chance.

Coolone you wouldn't happen to know which side the wiring loom you're talking about is on would you? Because honestly that is literally the last thing I think it could be. Something keeps saying CPS. It gets really bad after I have been on a long drive. I would imagine a failing CPS would produce these symptoms as it warms up.