So I re-jigged the wiring, its now using the 4xAA's for just the arduino side of things. The motors are now powered by a 7.4V 4000mAh LiPo stuffed in the butt of the gun.
The displayed voltage is for the LiPo, and the RPM counter now works heaps better, though it has a bit of trouble keeping up at full RPM!
So all my issues solved, and a nice little performance boost as well
Pics and a video soon.