Just bumping this back up. It's pretty much confirmed to be a problem inside the amplifier, as no matter how I adjust the inbound and outbound connections, the problem stays on a particular output channel (normally the right front). The problem affecting 2 channels at once seems to be gone. For now, the problamatic channel is routed to one of the stock speakers in the rear, so my upgraded speakers in the front sound ok.

Still need to swap around some input connections to get my fader controls working properly again. But for now, looks like the amp needs to be replaced. Now that I can afford a better one, I'll probably get one that can do my new speakers justice.