I agree with Mike Ryder. When I first read the symptoms my first thought was a fuel or ignition hick-up, not a trans issue.
I have been riding a 2002 R1150RS since May of 09 and my bike has done something similar 2 or 3 times so far. Basically it feels like it shuts downs for a second then comes bake to life. I can definitely feel the power disappear for a second. The first time wasn't too long after I bought it, and of course I was a few hundred miles from home. It freaked me out, but she ran like a champ for the rest of the ride. 15,000 mile later and it’s still screaming. As I write this it occurs to me that it hasn’t done it for quite a while now.
I’m not sure if my issue is spark or fuel (or even an issue), but until it fails completely, I’ll just ride. For reference, my bike has 27K on the clock.
Good Luck, and enjoy your bike.