Jason Sosbe: I guess IH added the mark on the drive shaft after fielding questions like yours on their "original" version of the Garden Tractor. As Harry enlightened us, there were no marks on the shafts installed in the first Cub Cadets. Congrats on the purchase of the creeper; I'm sure you laid down some serious coin for it.
However, I'm not sure I would cut my original shaft if I were you; instead, I would probably save it for a possible re-install.
I recommend purchasing some rod of the same diameter as your current drive shaft, available at your local tractor supply store, and cutting and drilling it to fit.
I know I have purchased a "Port-a-Drill" attachment for my 1/4" hand drill on two occasions which had integral V-Blocks like Doug Barnett mentions. It would work great for drilling the holes in your shaft.
One thing though, you would probably want to drill the holes first, and then trim the ends of the shaft back to get the proper spacing for the hole-to-end dimension. The reason being that the Port-A-Drill, at least, needs an inch or so on either side of the hole to hold the piece and keep it centered under the drill bit.
Just a thought. If I have time tomorrow, I'll post a picture of my "Port-A-Drill." I think they're still available.
If you plan on working your Original hard, you may want to consider getting a harder, stronger material for the shaft. I know Charlie's shafts are stronger than the original equipment.