Sounds like you may have broken the cable to the door or the pivot assembly...
I would say, take it back to the guys that did the body work.
Sounds like they did a good job and they should know how to fix it.
1996 2.5LT V6 Contour ATX
My Tour+help/info pics
E0 rims, Gutted Pre-Cats,CTA Custom Exhaust & Intake, Diablo Chip.