Thank you guys for your input.
Well, I'm going to use some liquid steel and see if I can fill in the groove and sand it down smooth.
I don't have the budget right now to replace the input shaft. The tranny has to come apart to replace the input shaft. A complete rebuild would be about $800.
Fortunately, the tip of the shaft that inserts inside the pilot bearing doesn't get much force and the pilot bearing doesn't spin that much... only when the clutch is disengaged from the pressure plate.
I have always only used the clutch to get in gear. when at a light i take it out of gear unless its a fast light
using the same Marlin 1200 clutch since 2002