Man, that's bad luck! You've replaced just about everything it seems. Hard to know where to look. I suspect a bad Pick-Up coil (ignitor) ... within the stator. Maybe swap in another from the other stator? They can be intermittent, from what I've heard. Maybe heat related?
Got to be heat related issue as she starts after cool down, no?
Could also be Rectifier/Regulator ... but I know you replaced that too.
But using 2nd hand donated parts ... its sometimes not possible to know if they are "known good". Not an easy situation ...
I know you wired in a bunch of switches in your dash. Could anything there be shorting or in anyway screwing things up? Also ... when you modded your dash, did you mod the ignition switch? I was thinking of that little hidden resistor (anti-theft) under the switch. It interfaces into the harness and goes to CDI ... if shorted or missing ... bike won't start. I doubt it is intermittent though. More mystery.
When you swap out the harness ... take care that little resistor.
But I keep coming back to the Pick-Up coil (ignitor)
Good luck ... I hope you solve it!