Another Mach 460 w/ no bass

2003 Mustang GT with a Mach 460 sound system. The system has no bass what so ever. Sound seems to be coming from all speakers, but no bass.

I folded down the back seats and took a look at the amps. I found that a small gray plug halfway between the 2 amps was unplugged. I plugged the wires back together and turned on the car. It now produced no sound. I adjusted the volume and heard a few popping noises coming from the speakers. I continued to fiddle with the volume and at some levels heard very low distorted music coming from the back speakers only at certain volume levels.
I took a few shots of the suspect wiring.
wire4.jpg

wire.jpg

here's a closeup
wire2.jpg

wire3.jpg

and a shot from either side so you know where we're looking at. This is in the trunk between the amps.

Alright, so I got in some new/used amps figuring mine were blown and got some different, but not better results. Got the new amps all hooked up, and plugged in the wiring harness pictured in the beginning of the post and turned on the system. I was greeted by popping crackling noises, so I turned the car back off. I took a closer look at the wiring harness and found it indeed did have some aftermarket wiring spliced into the harness.

I followed this wiring up and it spliced into the wiring harnesses for the 2 stock rear subs. I'm thinking this somehow bypassed the stock amps when the previous owner had aftermarket stuff, so I cut out the non-stock wiring, taped it up and turned on the car again.

I now was met by bass only, and only from the rear subs, and it was a tad crackly at that. No sound what so ever from any other speaker. (it's never simple is it) I unplugged that harness again so I could go back to my normal bassless music and tackle it another day.

I unplugged the harness to the amps again, turned on the radio, and no sound what so ever from any speakers. I tried switching back to the old amps with the same result. So I've made things worse, any help?
 
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