I have a 2006 Scalpel 1000 and a 2009 F29er Caffeine 1.5. In stock form, I much prefer the F29er. I just built it up with better parts (BB30 Afterburner crankset, Stans wheels w/ Hope hub, same lefty, better derailleurs) and the 29" wheels roll amazingly. Then I upgraded the DLR2 on my Scalpel to a Carbon SL110. Over a pound lighter and the actual fork functions WAY better. I also ditched the heavy Crossland wheels for some Crossmax SLRs (2lbs lighter!). Needless to say, the new fork and light wheels really transformed the bike and I'm completely in love w/ my Scalpel again. I would recommend, though, finding one of the new style Scalpel frames. The extra travel in the rear suspension is much nicer and I think you get an RP23 w/ that frame instead of just the RP3.
In short, the Scalpel is a wicked bike. Just don't skimp on wheels.