Leaving QP and WUP out of the equation, Rossi's best theoretical lap from FP1, FP 2 and FP3 (i.e. taking the best sector times he achieved in practice and putting them together for one lap) was 1.22.055, and his top recorded speed was 259.7. His best recorded lap was 1.22.168, or 0.113 secs outside his best theoretical.
Stoner's best theoretical lap (same criteria) was 1.21.405 and top recorded speed was 259.0; his best recorded lap was 1.21.461, or 0.056 outside his best theoretical.
So from practice Rossi was 0.650 slower than Stoner on best theoretical lap and 0.763 slower on actual best lap.
Rossi's QP best lap was 0.447 slower than Stoner's QP best lap.
In the race, Rossi's best lap was 1.21.713 - or 0.342 faster than his best theoretical practice lap and 0.455 faster than his best recorded practice lap. His best top speed was - golly gee - 259.7!
In the race, Stoner's best lap was 1.21.488 - or 0.083 slower than his best theoretical lap and 0.027 slower than his best recorded practice lap. His best top speed was 261.4.
The top speed difference was, in reality, sod-all.
I say Rossi had something up his sleeve from practice and he played Stoner like a fine violin for the race.
[edited to add differences from actual practice recorded best laps]
Road rash is nature's way of telling you you should have widened your entry