Stutter when accelerating hard 5000-8000 rpm range

[FazThou]

If i remember correctly when i done my old 99 r1 there are three bolts that are punched over that hold in the input shaft, make sure you get some new ones to replace the old ones in case you have to chisel them out.
Oh and some gasket sealant for between the crankcases.

Fowlers will do all the parts you need.

Good luck