Yes, the Pro motor mounts are lower than stock. In fact, if you cut off two ribs off the stock mounts they’ll be just as low. You will need to grind some off the chassis at the flywheel access hole from the bottom as you have inquired.

I left my roto start on mine. For the only reason that I could run out into the field, track, whatever with my glowstarter and roto start and restart my truck quicky and easily without the starter box. I also like to have at least two ways of starting my junk just in case one method fails.