Alright Jim, It looks like R11 resistor on the VR board has failed. I've been slowing testing everything and I'm back at the VR. Could the bad CVT1 have caused the failure? looks like R11 is in conjunction with T2 transformer.See if turning down the sensitivity pot helps. I labeled it "transient response" on the board, and it's the pot next to the voltage adjust pot. Normally you don't need to adjust that pot from where I set them during test, but your generator may have a little too much "uniqueness".
The second page of the instruction sheet explains how to make that adjustment, but turning it clockwise reduces the sensitivity and may help.