I think you may have damaged the amplifier first, which caused the amplifier to develop a problem that would cause DC offset. Then you damaged the speakers by connecting it to it again.
So you initially hooked it up incorrectly. It went into protect mode. You corrected the wiring. You listened to music through the iPhone, it sounded great. You played music from a turntable, it sounded bad. You started making changes to the system while the turntable was in use and the woofers stopped working while the equipment was on? Did you witness the event of the woofers ceasing to operate?
Well spotted Seth. My apologies for not checking every item of equipment the OP owned. You just can't trust anything in any post these days.
So he had an integrated amp and not a receiver, so he could not bi-amp he biwired.
So how did this happen.
So I do not understand how this happened if he wired it correctly. Leaving the jumpers in place would be no different to running two pairs of cables from one set of speaker outputs to one set of inputs. There would be no damage, as selecting A & B speakers just connects the two cables in parallel.
So I have to conclude, that he wired a pair of cables out of phase to each speaker, or more likely wired one left and one right speaker cable to each speaker. This is the scenario that would have most likely caused the DC off set.
Mixing up the polarity from a right or left terminal would cause a short circuit and I can't see how that would blow the speakers, unless the amp was damaged, and then when he removed the jumpers, the amp failed with massive DC of set and the protection circuit did not work, either because it was faulty or more likely was damaged in the shut down he now reports.
However getting a right and left cable mixed up with the jumpers connected would cause the catastrophic problem we have here, as the positives of the two power amps would be connected, and that is one of the worst mistakes you can ever make.
The far less likely possibility is that there was something wrong with the amp such as the speaker terminals miss wired.
That amp has had DC off set and so should not be connected to any other speaker.
Two blown woofers is absolute evidence of massive DC off set.
So that amp has been severely stresses and the best option is replacement since it is a new unit. Even with checking and repair, more problems down the line are very possible.