I'm not an audio expert, but I would suspect a connection, since the condition improved after you had the amp and head unit out. I would hit the connector and receptacles in each unit with some tuner cleaner, plug and unplug the connector several times to loosen any corrosion and crud, then more tuner cleaner. See if this helps.
Bill
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BJ's BlackBox -- 2001 Boxster
1997 SAAB 900S Turbo
1980 Maxda RX-7
1974 Fiat 124 Spider
1976 Datsun 260Z
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