The drivetrain is a little weaker, but it should stand up to the force of the BL.

I think it is best to leave it in 4wd mode. When I was testing mine, the front drive shaft fell out and it sucked with only the rear wheels being powered.

The ideal setup would be to have the weight of the batteries evenly distributed, but having 9 on one side doesn't seem to be causing any trouble. If you are running lipo, this woudn't be much trouble because the battery would be so light it wouldn't matter too much.