There is a pretty helpful thread on 999 "issues/problems", try the search. I posted to that some time ago. A lot of good info when looking at a used 999. In summaru, 2005+ deep sump engines are the best bet. Not to say the older versions are not good too, it's just hard to find fault with the 05+ engines, they are very solid and well sorted bikes, except for the weak clutch master which in turn leads to tons of "why does my bike stall of shift notchy".
BTW, the clutch master is an easy fix. Two bolts on the handle bar and one bolt on the hose, remove the brake lever and replace with the master with new brembo of other of your choice. Once that simple fix is made, and you check the coolant hoses which are subject to leaks, your good to go.