Hi!
Is there an external amplifier anywhere? (Possible if you have any sort of a "factory premium" (in terms of price) speaker system...)
Have you made sure all connections are good?
Wiring is possible, and honestly, it seems like the most plausible option if you have already changed head units, examined the harness and speaker connectors and replaced the speaker. Remember that the wires do take a lot of flexing and abuse from the door opening and closing. They also take thermal extremes in summer and winter.
Try this stuff, and see what happens!
Best of luck!
William the Guesser