BINGO! I put some cheap new copper plugs in and it's running really good now. So in the end I think the intake cam being off one tooth was the vibration it had and the cleaned (dirty) plugs was the issue after the TB was corrected. Awesome. It warmed up all the way and runs good at all temps, with an occasional pop here and there to remind me it ain't perfect. I'll drive it tomorrow.Dirty plugs are a huge diagnostic red flag. If your spark plugs are sooty black it is time for a trip to the garbage can. They will almost certainly be contributing to the crappy operation.
What a saga. Thanks for hanging in there with me guys.