I have finally tracked down the problem. It was indeed my damn HU. I received my new Krypt 4200 EQ today and installed it back into the system. First I tried it by just plugging in my mini pin/RCA through the EQ to see if I had noise through the tower speakers. The speakers sounded crystal clear. Then I plugged in the RCA from the HU into the EQ and I had the noise! Same noise I've been hearing all along. Sooo, with all my frustration carrying on and a vacation coming up, I couldn't go without towers, so I ran down to car toys and picked me up a new Kenwood KMR 440U. Brought it back home, replaced the currect HU with the new one, hooked everything up, and wala! NO NOISE... So it turned out to be a bad HU. I hope no one ever has this problem, cause it was a PITA tracking down. I guess the worst part about it was in the back of my head I really really didn't want it to be the HU that I had just installed in the boat 2 months ago. I was trying to blame it on everything else, and because not everyone just has extra HUs laying around. I fortunately had my stocker, but for some reason it was reproducing the noise as well, so that must be a bad HU as well.

Hopefully this thread will be useful to others that experience noise through their external amped speakers. I'm not saying all noise is going to be the HU, but if you have similiar noise as I was experiencing, don't be afraid to blame it on the HU after checking everything else. The noise I experienced with this bad HU is while on the water, there was hissing, poping, and extreme krackling as the boat was rocked and bounced around by wakes. With the boat out of the water I was experiencing hissing, as well as being able to almost hear the HU thinking, like I've said before, CD starting to spin, changing songs on the CD, etc.

The HU is still under warranty, so I'll be sending it back for a replacement. The new RCA ($150) I was able to return. I may return this other HU I have, or keep for a spare. In all I don't believe I'm down much on $$ from troubleshooting, so all is good. I'm happy and ready for a week vacation! Anyone wanna buy a boat? LOL