Everything looked intact in the amp wiring, I just had the one plastic panel off that you have to take off to get to it. If you change the balance to left and crank the volume you can hear sound (but very static-ey) in at least the sail speaker; I'll try swapping the speakers tomorrow too though.
On the blue wire, it is the amp turn on from the aftermarket radio's harness to the OEM-to-aftermarket adapter (Metra) harness; it just fell out of the Metra's connector and I had to push it in and tape it so it wouldn't fall out again. That restored the sound back to how it was with the stock HU.
I wish they made an amp bypass cable, all they would have to do is duplicate the socket on the amp and put in 8 pins. If the speakers work when swapped I'll probably just bypass the sub and install new speakers; just hate to chop up the factory wiring.