It sounds like you are figuring it out, but to clarify, The over speed control just turns on and off power to pin 1 of the governor control, if you have power to pin 1 than the over speed control is not the problem and you need to follow the trouble shooting procedures the linked manual. (also note pin 2 is ground) In my opinion with the intermittences of the problem and the fact that it has tripped the over speed (presumably without actually over speeding) I would be looking hard at the magnetic pick up in the PTO, that is a common source of all kinds of problems. In case you didn’t know they are available from Muncie, I just replaced mine and the cost was about 80 dollars.
Hope you figure it out, Justin