Well,
I know the rubbers are on correctly.
Moe reminded me to check the vent on the tank. I might have pinched it.
The bike went from lean to rich.
That is expected.
On the pilots, I adjusted it down first to see if I could lean them out and then back up to 3 turns out since it didn't seem to make any difference.

I still have a feeling that the carbs aren't quite clean. I bet there is a passage blocked. But I will reserve that judgement until I can't get this troubleshooting to work.
This bike ran previously with the way it is set up before it sat for a couple years and then the carbs got lacquered up. So I know it should not need shims, or jet changes.

But I am going to try both electrical connection checks and the potential vacuum issues first.