If you have the 50/54 forks like the monsters then you would need 50mm clip ons.
I would ask over on Ducati.ms about the stem lengths. Not exactly sure myself as to what the different stem heights are, for swapping another duc front end on that's the place to inquire.
As for the top steering stem nut, you will need the special removal tool. They can be found on ebay for a couple bucks pretty cheap.
R1 won't work as all later Ducati's basically all run 35mm ID stem bearings. Only stuff that really fits are other italian bike stems like Aprilia, MV Augusta, Bimota, etc.
If I recall pretty much all japanese SBK bikes are 30mm ID.
Somewhere on there is a big list of fork sizes and stem bearing sizes. Think it's stickied in the suspension section.