Just wanted to give a final update, in case anybody has a similar problem in the future.
1) The initial dead battery was because my subwoofer amp wasn't shutting down properly (cooling fan was running 24/7), and because my remote starter was staying active. Both issues have been corrected.
2) The other issues were because of the CANbus system. I have an aftermarket stereo. I didn't bother to post about this because I didn't think it was relevant- however, the jumpstart fiasco fried the CANbus connection to the car stereo to the point where this eventually took down the entire CANbus network. This was solved by disconnecting the battery for 15+ minutes (in my case 35), and replacing the CANbus connection to the car stereo. Crutchfield was very generous and replaced this free of charge. (In case it matters, it was the GMOS-01 device by Metra, with the AXXCESS label. Crutchfield has stated that these are actually very reliable units., but I'm on my 3rd now.)
3) While I was waiting for the new GMOS-01, I had to remove my stereo (and the GMOS-01) and the car ran fine. As stated by industrialfish, the process is to find the bad node on the network and remove it. Unfortunately, finding the bad device is very difficult except by trial-and-error, and in my case I was lucky because it was the one place I was familiar with on the network.
My next OBDII scanner will also have CANbus scanning capability!
Thanks everyone for your help.
-BC