This sounds like the stepper motor is failing with heat. Given the Hz signal is straight from the alternator.... a loss of the signal would intially cause the unit to overspeed. (Wiring from alternator to control board problem maybe... also heat related)
The only thing that made sense to me is a problem in the 10 Ohm freq sensors or the stepper motor.
Noting you have changed the control board and your still having overspeeds Look at the the Hz sense portion. I would bet your shutdonws are being initiated due to over-voltage vs over-speed. That you may have to sort out.
Sounds like a long day... of troubleshooting. 5 - 6 hours wait and then PANIC just to duplicate it!
Hopefully you have the service manual. I have the one for the 15Kw and Up.. but sense circuitry is pretty much the same.
Sense circuit...
* Measure resistance across any combination of orange, yellow, brown, or black should read approximately 20 OHMS.
* Measure from red to any other lead should read 10 OHMS.
* Testing from any lead to stepper motor case should read INFINITY.
Orange or black to Black or green One leg... 20 Ohms
Yellow or Red to Brown or white 2nd leg 20 Ohms
Again Stepper motor or sense wiring / windings... is where I think the problem lies.
Good luck and I am willing to keep taking stabs at this. 40 years as an electrican here.
Thanks for choosing FixYa,
Kelly