That is a good idea. Plug anything you can into the RCA's of the harness. I would even try each channel separately. It would then completely rule out the empeg and sled (at least the RCA outputs). If you still get the noise, maybe you could take the signal before it goes to the Bose amp, and try it with an aftermarket amp. That would tell you if it is the wiring, or possibly the Bose system. I haven't ever pulled my Bose amp out, so I don't know how difficult this would be to test. If with your MD you don't get the noise, could it possibly be noise from the power? Maybe try wiring the empeg directly to the battery (be sure to fuse it near the battery) rather than through the cars wiring.