At first I tried cutting the shafts with a metal blade on a chop/miter saw. It cut fine but was only able to get close enough to end up leaving about a half inch of the shaft still on the motor. It also made the shaft extremely hot, which probably wouldn't damage the motor, but I didn't want to take that chance again. Since something else was needed to finish the job I decided to just use a hacksaw. With it, there was no problem getting extremely close to the shaft housing. It only took a few minutes to trim off the remainder of the shaft, then a couple metal files were used to clean up and smooth out the finished product.
The same process was repeated on the other motor shaft, minus the chop saw. Fairly quick and easy. Definitely easier with two people so that one can hold the motor while the other saws. Now onto getting the Battery Boxes to fit. That requires grinding the tops of the motors, and a cut or two to each box as well.