As long as your still using the Monsoon amp your gonna have to have a GMOS-01 harness to keep running the factory amp unless you go through a whole bunch of research on wiring and I still don't know that you could make it work. I've had mine both ways( with the monsoon amp and bypassing the amp) currently in the 04 that I have now I have replaced everything with aftermarket equipment.
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Actually with the Monsoon system you would need the GMOS-04 harness not the 01. The 01 harness is for non Monsoon systems, Or if you wish to bypass the Monsoon amp and wire your speakers directly to the headunit.
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