I have a spare rear grip which would be useful to me if I can shorten it a bit. If I cut it,
1. What's the best tool to use for a clean cut, and
2. Once cut how do you clean up the cut end such that it doesn't appear cut?

Dan,
I use an abrasive cut off wheel on a chop saw to do all of my blank and grip cutting. It will work excellent for this task. I can not help you with question #2 - with respect to finishing the cut end.

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For the abrasive cut off wheel, I use a tool room 1/64th inch thick cut off wheel. This very thin wheel cuts quickly and removes very little material during the cut. It also cuts extremely cleanly.

Good luck

Cheers Roger! The cutting wheel sounds like the ticket.

How do you hide the cut edge if that edge is to be immediately adjacent to the reel seat?
I used a decorative winding check on the previous rod at this juncture and it blended very nicely. However the grip in that case had not been cut and the woven edge of the graphite rolled down over the leading edge of the grip thereby covering its underlying rigid foam. The grip had a very slightly wider outer diameter than the winding check.

Dan,
I shortened and mortised a carbon fiber grip using a Dremel tool with a sanding drum. I placed the grip in my drill press and rigged the Dremel tool vertically on the drill press table, which I could rotate into the spinning grip. It resulted in a clean stepped diameter of the grip. After I mounted it into the reel seat, I tinted (black) some Rod Bond, which effectively covered the seam between the grip and the reel seat.
Although I liked the look of the CF grips, I didn’t care for the feel of it while fishing, so I cut it off and replaced with cork.

Just Don't Breathe that dust! Use a respirator please, Jaa

I use a cut of wheel in a Dremel in a vice and turn the part.

I've used a Portaband. Seems a bit easier than a cut off wheel. Covered the rear cut with a EVA butt that worked out pretty well.

I use my lathe and micro parting tool. This is with foam core carbon grips.That gives me a nice square clean cut. I have the glued on many different materials to finish it off. The real trick comes trying to make fighting butts or rear grips without a through hole ( no plugs or butt caps ).