I have a 2007 dodge charger rt, the engine will start and runs for about 2 seconds then shuts off. the power windows and door locks are not working. I get a code u0001 with my scan tool but the scan tool will not communicate with the door module. the scan tool will also not connect to the pcm. I replaced the pcm with a used pcm that i had programmed and flashed for this car but still no luck.

 

That sounds like SKIM, like your SKIM and PCM weren't properly mated. To put it simply, you crank it up, it starts, it shuts off immediately because the PCM does not get the correct signal from the security module. If this is the case, if you keep trying to start/run it, it will eventually lock the PCM.
1. Was the PCM installed correctly (is it the correct one) and all connections good and tight?
2. Was this a mail order PCM or flashed in the vehicle?