Ok, made a battery tray, used some kydex (thanks rchippie) and cut out a shape. Took the heat gun to it and folded the sides. Used a carbide bit and cut slots for the velcro to go thru. I will have to make a pair of al spacers to raise it up to clear the dirt guard. Pics show it mocked up with some scrap kydex as spacers.
I will also move the receiver to the top of the servo, and clean up the wiring. I need to make a plate for the quark to attach as well. So far I have not drilled any holes in the chassis, and do not intend to!
Charged my batteries back up from the initial run, which was 12-15mins long. I put back just under 1100mah, so I think that 20mins or more will not be out of the question. I will give the align motor a few more packs, then switch to the hacker 15l b50 and see how it does.