I can tell you that they are very very close to each other. Now let me explain:
My 749 has a assymetric remus with a PCIII and the headlight unit has been removed. Everything else is stock. I run with 1/3 tank of fuel and lightweight knockoff fairings. Gearing 14-41
My buddy's 996 has Termi slip-ons, Gearing is 14-38, everything else is stock.
I'm about 160 naked and he's prob 180.
So when you add it all up my bike's down about 15 HP??? And I'm prob about 30lbs lighter in total...Give or take. We run the same tires and same pressures.
All that being said he has followed me for many laps and I've followed him for many laps. I think that there is a slight advantage to the 996. The torque out of the corners is the key for his advantage. However if I'm in front on the 749 - I have to make a mistake for him to pass me into a corner after a good straight. Miss shift or whatever. That little bit of extra power can get him by most average early to mid 2000 600's. My 749 can keep up but its tougher for me to pass. 600s can pull away slightly from the 749 on the straights so its an even greater distance to make up when the brakes come on.
When I'm behind him I can keep up but its pretty tough for me to get by...he's got to screw up pretty bad. Both bikes are set up to feel pretty much the same on the track...(I'm the suspension tuner for both - wink wink)
If the 996 were a 10 for performance then the 749 is a 9 or 9.5. However the 749(999) series in my opinion is way way more reliable a track machine. There just seems to be more issues that creep up with his 996 and my 749 just keeps on rolling...gas and go!!!
BTW they are both a blast to drive on the track...Like sex with identical twins...similar, different, and tons of fun