Ok, im glad the flickering lights are normal, i was worried it had another problem.
I moved the limit switch back for the Y axis. The head still touches the frame at the front of the printer, but the stepper does not stall anymore, Is this ok? Im not going to be printing that close to the edge anyway, but will it affect anything else now i have moved the position of the switch?
Ic's at 80*c is a little to hot for my liking. I bet stepper drivers at 100*c would be getting close to thier thermal design limit. Don't forget i was measuring the back of the board with an ir gun, not very accuate on a tiny surfacemount. The chip would likely be hotter.
I will get the new probe as you suggest, it would be better than getting a new unit.