Okay, first off, if it sounds like you pulled your own wire from all your speakers, and also provided your own power and ground, what leads are you using from the factory wiring harnass? :) Or are you using the power and ground leads through the harnass to power and ground the empeg?

Yes I pulled all new speaker wire and power and ground for the amps. The empeg itself is running from the stock power and ground through the mess of adapters I mentioned. It is not grounded to the same point as the amps.

Okay, so you pulled out the cheezy factory Jeep roll-bar speaker wiring and installed your own and pulled it into your trunk? I assume your amps are grounded to the same position.

Yep, they lasted about a week. Both amps are grounded to a distribution block in the 'trunk' which is grounded to a seat mounting bolt.

I have one tiny 40W amp powering the front and roll bar speakers

If I had to place a bet I would say that this is your most likely problem. With that weak of an amp you probably have the gain cranked beyond what the amp will do without causing excessive noise. I am pushing about 60 watts/channel to my speakers so the gains on that amp are way low.

I would definately try wiring everything through your better amp and see if the noise disappears.

-Mike