If the window is going up and down with the key, that's good. It means the power and ground are good for the door module.
Check the connection between it and the door switches; check out the pinouts here, page 95 Volkswagen Transporter T5 (7H) - Wiring Diagrams -vw-t5-2003-wiring-diagrams-eng.pdf J386 and E40 E81
Does the lock door button still work?
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