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2000 VW Jetta!?!?!?

My wifes jetta will sometimes “turn over” but will not start. some symptoms i have noticed are with the drivers door; when lights are left on it will not ding when door is opened like it used to, also when key was turned of the windows/radio were still active until the door was opened now they dont turn off at all until car alarm is armed. I thought it was door switch but the alarm still arms properly; will not beep to signify alarm armed till door is closed, goes off when it is opened. Could there be any relation to car not starting and these symptoms. Just recently had motor rebuilt and did not have problems until this was done. Also replaced the fuel pump relay and cleaned all the ground wires i could find. Any help would be appreciated!