Sub problem, questions before I start spending cash

The problem started back when my voltage regulator blew and I overcharged everything. Ever since then(new alt.), I have been having a problem with my sub. I have since replaced the head unit, and have gotten another sub.

Details:
When key is in the ON position, the sub will hum a bit, and pop when the car is started.

It hits with inconsistent power, even during the same song. I will be driving along, have it hitting hard, then all of a sudden hit lightly for a while, then back, and so on, all during the same song.

The only possibilities I see are either the amp(which didn't blow its fuse during the overcharge) or the RCA cable(only because someone else told me that). I don't understand why it would be the RCAs, considering they just send a signal, not 12V.

Any suggestions before I go buying anything? Any help would be appreciated.

Thanks,
Chris