Could be the idle controll sensor. But your on the right track. Clean the throttle body and map or maf sensor with the correct cleaner's. Get it at the parts store.could also be the pcv valve is carboned up.
Most likely a break in the wiring harness in the hinge area of the liftgate. Check for power and ground. If you don't have it, it's a wire or ground connection issue.
What do you mean disprogram your engine of a 03? If you mean will the engine still operate the same, yes it will. If anything, you may need to reset the radio clock (if you have one), maybe reset the radio station presets, and on some vehicles, may need a car code to allow the radio to turn on.