Update:
I took the pack out of the car again for more testing. This time I did a self discharge test of all the subpacks, charging them with the superbrain, recording their capacity, letting them sit for a week and discharging them and recording mAH returned. I was expecting to find a few subpacks with very high self discharge rates but this didn't prove to be the case. The capacity returned on discharge for each subpack after a one week rest was between 77%-84%, not an exceptionally wide spread to my eyes. Before I put the pack back in the car I charged each subpack again just to be certain they were all full and drove the car. It set P1449 before I even made it out of second gear.
So now that I've established that all subpacks have good capacity (>6,000mAH) and similar rates of self discharge, the only other potential issue I'm aware of would be that some subpacks bench test well but cannot handle the high discharge rates they are subjected to in the car. I read on another forum about another testing procedure which involves using a high current battery load tester to test the subpacks under loads similar to actual driving, and monitoring the voltage of each cell in the subpack to see which ones drop out. Is anyone here familiar with this test, or has anyone done this and had success? Here is the load tester that was used for this test:
500 Amp Carbon Pile Load Tester