Dude, DON'T CUT THAT BOOT! You don't have to. I pulled the dust boot off the original shifter and put it on the Pro 50. It's a little tight, but it will fit. I then installed the "floor board" boot (uncut, of course) over the shifter handle. I pulled it down 'til the shifter hole nestled between the two shifter handle bolts ( If you push it down past the bottom bolt it might bind).
This way The shifter mechanism is protected from road grit by the old shifter boot, and the floor board boot remains cherry. Plus there is one more layer of rubber between the cockpit and the tranny, Making for a quieter ride!