Found this site earlier, then lost it as it seems I never posted it. Three hours of Google-fu later, I finally found it again: http://repackr.com/
The site lets you put in your individual cell capacities, and from that it will build a balanced pack for you. Slick.
The cells have been chilling out fully charged for a 2 months now. Ryden measured the voltage of each. The ones which had decayed the most were set aside. The spread of best to worst for the remainder was only about 0.15 volts, so I'm pretty happy about that.
Ryden then sorted the remaining cells and input the cell capacity numbers into rePackr while I worked on the drive-train.
We are out of time for today, but we should get to finally welding up the packs tomorrow. Whoot.
<EDIT> Added in some other cells I had to replace the lower cells here, and recalculated the packs. Average capacity went up to 10587.
Welded most of them together today and drained the battery.
We still need to go over three of the cell groups again with some more spot welds. Tomorrow.