Hi Kyle, I had the same problem.
the dog's that hold it in gear are worn and cause it to slip in and out of gear and everytime it slips it makes it alot worse.
the first time this happened to me was with 7000 klm on it and I had to replace 3 gears, selector fork, shift shaft and the shift drum, I got the bike back and after about 1000 klm and $1600AUD it has started doing it again.
in my opinion this should be a re-call, the box just can't handle the herb's
other suggested re-calls:
those ****ty damn rearsets that bend everytime you do a stand up mono
the crap valve guides that make that ticking noise.
they are a great bike to ride but I can't keep up with the assosiated costs, test riding the GSXR this weekend
Rob