The problem of the light should not be with the wiring to the door itself, but rather with the door pin switch on the "A" pillar.
The wires and vacuum tubing for the door pass right behind this switch and it is a real pain in the ass feeding it all through from the foot well area adjacent to parking brake to the opening in the "A" pillar.
I would not be surprised if the extent of the problem is the ground wiring connected to the pin switch was knocked off/loose by all the manipulations of the door wiring during the door change process. It is relatively easy to pull the pin switch out and check the connection; just squeeze the top and bottom parts and pull out. The check that your wires are connected.
Here is a thread on the switch itself.
http://www.peachparts.com/shopforum/diesel-discussion/289097-door-light-buzzer-switch.html