Well I finally had a chance to do some troubleshooting (in the rain) this weekend. I disconnected the empeg RCAs from the amp and powered cycled the empeg. It still made the noise, so I ordered a new amp. I'm replacing the old 2 channel kenwood with a 4 channel memphis mca 2004. Hopefully this will solve the problem.

I called the guy that installed my empeg and amp a few years ago. He said it sounds like an amp problem, but I should also check the amp ground wire (he said he ran it to one of my seat bolts), apparently there is a ground separate from the negative on the power section. I have to take my seats out to check that, so I figured I'll just order a new amp...