My shop fixed my car today...
The fan clutch was the cause of the over heating problem.
The rought idle, stall etc. was the coil wire. Somehow it was damaged, looks like the fan blade hit it. Not sure how it got that way but the core was slightly exposed. The coil wiring is now running through a rubber hose that is just under the air cleaner.
Besides that the air mixture was adjusted too.
Oh and the thermostate was replaced, even though I just put in a new one...I don't think that had anything to do with it but when you are trying to find a problem I guess even the smart guys start with the easy stuff first.