You should never fully discharge Li-ion batteries. For the Li-ion 16340 cell chemistry, discharge to a minimum 2.75V; probably safer not to go down below 3V per cell. Charge to max of 4.2V per cell. Charge has to be constant current and constant voltage. You need to monitor the cell voltages, so some form of BMS (Battery Management System) is needed. To be honest I think you are wasting your time with these cells. They are probable not capable of supplying even 1C rate. So with only 6 cells in parallel, the battery will not have enough capacity to run the hub motor. These 16340 cells are meant to be used in torches not power a BLDC motor.
If you really want to build your own battery; it would be better to go with A123 26650 cells, LiFePO4 chemistry. A123 cells seem extremely robust and stable. They have a high C rate; although the cell capacity is only 2.3Ah, they can support at least 30C constant discharge. LiFePO4 cells are nominally 3.2V; they can be run between 2.5V discharged and 3.65V fully charged. You need 12 in series for a 38V battery, 43.8V fresh off the charger; and as many in parallel to increase the Ah capacity to your requirements. They are more expensive than the cells you have been experimenting with but you can get them on ebay. Like others on this forum, I have used this supplier
OMG who seems reliable and price wise about the best. I have put together a battery with 72 A123 cells, 12s6p; similar construction to jerrysimon. He has a full description of his
small A123 battery build, well worth reading if you want to go for the home made battery.
Of course your other option is to get a readymade battery form
BMS Battery or
Ping etc.
But you sound like an experimenter to me, so.....
Cheers
Chris