You can try a continuity check from the door harness back to the radio... Check both + and - leads to see if they're making the trip to the connector on the radio. Remember, the speakers ARE NOT grounded. The amps use a floating ground any more, so there will be no connection from the speaker to the body of the truck. You already know the speaker is good, so the suspicions of the wiring are probably justified. A meter will tell if the wiring is intact.

It's very unlikely the factory harness has a polarity problem. Muddy sound at low volume usually indicates a blown speaker. Folks like to turn the volume up, which produces distortion. Distortion kills more speakers than too much power. If you try another speaker (at low volume) and it's muddy as well, you may have lost a channel in the radio. That will produce muddy sound as well.

The issue of broken wires in the boot... Is the harness too short?