Well dyin at stop lights, does it start right back up, and if you put it in gear it just dies again till it cools down? That would be the TCC, if its dying and just restarting, if you have a stock chip there freakin awful and make the cars die all the time, my TGP with all new injectors xover ect ect with the stock chip was halfway undrivable. If anything try cleaning the idle air control valve and its port on the front of the throttle body.
So the pump motor just wont stop running? It probably has a bad pressure switch thats not turning the pump off so its overpressurizing the system and blowing the cap off. if you keep this up it will destroy the pump.
The window motor coudl be the motor, switch, or real common is the wires going through the door jam kink and break in the rubber insulator, youll just have to investigate, typical old car shit.