After fighting with this stupid ign stumble, I think I got it fixed! Here is what I did before changing to CoPs.
1) New BKR6ES-11s gapped to .035 (hesitation went away quite a bit, still there)
2) Changed plugs again, this time to BKR7ES gapped to .030 (no noticeable change)
3) Changed the coil pack, stumble appeared to go away, then it came back in 10 miles.
4) Changed the exciter, did nothing.
5) re-installed stock ECU with Bipes, NO stumble :(
At this point I was quite frustrated, and the stumble would randomly come and go. The stumble was more prominent in the 4k rpm and up range. So following Braineak's write up on CoPs I installed a set off an ES300. And sure enough the stumble is gone! Car will now rev to red line while in 12 psi boost with no hesitation or stumble. I then purposely bogged the engine, no stumble, took it for a 10 mile cruise, no stumble.
With any luck at all the stumble is now gone!
I am not sure what could have been causing the stumble. The only thing I did not change were the wires. But they have less than 10k on them, and I have never seen wires cause this issue.
CoPs being built
CoPs in Miata