Hi ONF, have you tried a multi-meter on the pins of the amplifier to see if all the channels have output. the low end muffled my be coming just from the door speakers, which are base. also as i have done with mine check if there is power feeding to the speakers themselves. on mine as you may see on the other tread i am checking to see if i have a short somewhere.
i have a red light in just the one fiber optic on mine also, i think the other one is from head unit to amp and if you take it off the amp the other one will be illuminated. one side for head unit to amp and the other amp to head unit.
sorry i can't offer much help, i hate auto electric gremlins.
