[Jeph]

Perhaps while replacing the window regulator, the battery was disconnected? That justifies entry into the front trunk. Could that also reset some of your stereo settings? Or will cutting of the power leave it exactly how it was? I don't know.

And this may be a stretch, but perhaps while removing the battery cover or something the wires were unplugged some how on the amp -and when reconnected were swapped.

Just a possibility...

(Now I want to see what your trunk looks like to see if I can get to the bottom of this. Post a pic if you're REALLY bored.)