So I just started trying to get into this and I've run into a slight issue, here's where I'm at. I can copy the factory chip and burn a new one and it runs just as good as the factory one. I have the definition from tunercats ($88 for the LHO engine) and the factory tune reads in there as it should. When I change anything even if it is just to re-enter a factory setting (so should be no change other than being edited by the program) then burn it to a chip and install it in the car, the car won't idle and the coolant fan won't turn on. Am I doing something wrong or missing something like in settings or something?

 

Sounds like something in the burner settings. Compare the edited BIN to the stock BIN and see if they are the same. Then move on to checking the burner setup parameters (buffer and PROM affsets and such).

RBob.