It doesn't matter what rpm your at really, I've been doing for about 5 years on my GIXXER, and when I picked up my R1 this weekend, it was the same way, I didn't even think about it.
I suggest to always use the clutch on the 1st to 2nd, but after that, just accelerate, and the gear box is under load, it doesn't matter what rpm your at, put slight pressure on the bottom of the shifter(it will not move if you are under throttle), when you reach the rpm you want to shift at, let off the throttle for a fraction of a second and then get back on it and the shift lever will move into the next gear. It works at any rpm. As soon as you unload the tranny, the shift lever will move.