The amps are pulled directly from the battery, whereas the empeg is tied into my wiring harness, and I'm not sure how many places it goes before it hits the battery. Could this cause a problem?

Not if it wasn't a problem with the Mk1. The only place this might be an issue is if you're grounding through the Empeg chassis only (i.e., the ground wire on the connector isn't going to a solid ground).

Try a "divide and conquer" approach to narrowing down the problem. Pull the sleeve out of the dash and disconnect all the audio plugs. Try plugging something else into the amps (such as a walkman's line-out) to see if the problem is the amps or the Empeg. If it's the Empeg, try connecting one RCA jack at a time (with the sleeve still out of the dash) and see if it's a specific connection. That sort of thing.

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Tony Fabris