Ah, clarity, I apologize.
The choice of the six cell packs made it easier to fit into the panniers as well as wire for the balancing charger and battery medic. I think after all of this, it might have been better to go the same way you suggest (and Morph does).
Took the bike down to the local bike shop as I promised the owner for a test - blew the 20A fuse before I got out of the driveway, but I had anticipated that and replaced it with a 30A. I went about 6 blocks as fast as allowed by law (disappointing - I've been faster pedalling) and got it home. Lugging the bike up and down the stairs with the packs mounted was a lot of fun (not doing it that way again)
When I got back, the cells were back to 3.36v, the Cycle Analyst said I had used .5AH - not sure if this is normal but there was 1 block killer hill and there is a lot of weight, so.... This is something I am going to have to qualify with a longer ride on the weekend.
I realize LiFePO4 cells have a flat voltage they stay at for a long time, and I'm thinking 3.36v is it, no matter what voltage I charge the packs to.
Hooked the 36v charger up and it ran about 20 minutes while I watched the cells. After it was done, all the cells except my "problem child" were perfect 3.65v and the low one was 3.54v... So there definitely is a benefit to starting with a balanced pack.