Ordered up a clutch kit yesterday, comes with clutch disc, pressure plate, pilot bearing, throw out bearing, and a new slave cylinder.
I'm not going to worry about the input shaft on the tranny right now, I'm sure the bearing is wore a bit but still in tact. I think it will be fine. And like Mr_Rich said, the pilot bearing should support the shaft.
I decided to go ahead and get a new save cylinder just to eliminate any near future problems and since my truck uses the newer internal slave I did not want to put every thing back together and just have to tear it apart again a few miles down the road.
I will be sure to let you all know how it works out.