There were no speaker wires in the doors. The installer basically re-did everything as he needed to wire in the amplifier and speaker cross-overs anyway.
It looks like he drilled a hole in the body to bring the wires into the door hinge area through a round grommet, and then went into the door through a new hole in the bottom of the rubber seal that houses the factory wires where they enter the door. Clear as mud? Here are a couple of pictures.
This pic shows where the speaker wires come out of the body going to the door. ( the image is the right side door, and is rotated 90 degrees to the left for some reason)
This pic shows how the wires enter the door. ( also right side door but rotated 90 degrees to the left for some reason).
Here's the amp and crossovers in the trunk. I made a cover out of plywood with vents and some spacer blocks that goes over the amp to form a false floor so you can still put stuff in there without smothering it.