I have little experience on a 999 but my 916 was more uncomfortable than the one 999 I rode and I made it in to a very comfortable bike for long trips. For years I couldn't even ride it because of a wrist problem. This is what I did:
1) Cycle Cat risers
2) Put a cheap plastic "cramp buster" type of device on the throttle
3) installed more heat shield under the seat
4) installed a Sargent seat
5) yoyodyne slave cylinder for easier clutch pulls
Then I installed some Ventura luggage and the bike was extremely comfortable on long trips and didn't sacrifice any performance.