Pulled the door trims off to see why the window wouldn't wind all the way down. As it turns out, the crossover for the speakers was in the way.
After a bit more looking, someone along the line done an upgrade as it's all Hertz speakers and crossovers, with tweeters in the heater vents on the door.
Must have gotten pretty wet in there at some point because both crossovers were all but fried, which explains why the sound comes and goes over bumpy roads.
Tested the tweeters by themselves and they're dead as well, but the woofer sounds pretty good when plugged directly back to the headunit.