I just did mine this fall, on a Minn Kota Powerdrive V2. I bought a new shaft, planning on cutting it, then replacing the original. However, once I started trying to take off the old shaft, it was a royal PITA. I decided to just cut the original shaft with the wiring in place. I took a hack saw, and carefully cut until I broke through the side wall. Then I rotated the unit 90 deg and cut again. I did this on all four sides, then cleaned out the little pieces that were left. Each cut took less than a minute with a hand hack saw, and the end result was very clean. I would definitely do it this way again. When I was done, there was only a very small abrasion on one of the jackets where the saw hit the wire, absolutely nothing to worry about.
I then aligned the head with the power unit and used the existing cross hole in the head as a drill guide for the screw. Again, easy as pie.
In the end, I did it this way because I had the other shaft available in the case that something went wrong, but I never needed it.
Good luck with yours!