Update. The bike has been sitting while I've been doing the work on the new tank. All the banks read around 3.95V per cell, and I took it for a spin on Sunday. The cells were reading around 3.75 or so when I got back in, on the banks I had the cell loggers on (still waiting on connectors, so they weren't on all the banks).
Got back and started topping them up... and got another error message on one bank. The #1 cells on one bank were all reading 0. (Three individual packs.)
Figure these were just packs that got weakened by my previous mistake, and it took a while for them to fail... but I'm still amazed that all three fail like that. It sucks. I think I'm going to start doing what Kyle suggested, and taking a few apart to see what the hell is going on.