I'm not sure you posted how many miles your dad put on the bike, but you should bear in mind that these bikes take at least 20,000 miles to get broken in. As long as the oil is changed, and the valve clearances checked the mechanical workings should be good for well over 150,000 miles. Remember that you are essentially dealing with a car engine here.
Change the o-ring on the output shaft and do a clean and lube on the clutch splines.
Check the air filter for mouse nests, throw in some new spark plugs, and balance the throttle bodies. Run a couple tanks with Techron through the injectors. Check all the rubber bits for holes and cracks. Beyond that there isn't much the engine needs if it's got less than 100,000 miles on it.
About the transmission. If the grub screw is loose this is a really good time to address it. Does the shifter flop around freely? If so, how much? My RT had shifting problems because that screw was loose. You don't want to go into the transmission after the bike is put back together.
Have you done or made plans to do all the maintenance, brake bleeds, fork oil, cooling system, etc.