Never done it on an R6. That has the stacked transmission. But, a buddy and I pulled the motor and had the parts out in a few hours. (I had done the process before, though) We ordered the parts ($160) and put it back together in an evening.
I still highly recomend that you pull the left side case and check out the rest of the shifting mechanism first. It may be in there. Both times that I had to fix the bent shift forks, it would still shift, it just wouldn't stay in second gear.
If you do end up pulling the tranny and shift forks, look for very minute wear on the sides of the shift forks. That is what indicates that it is twisted. You won't be able to actually tell that it is twisted visually. You can just see where the gear that it pushes has been rubbing against it.
If Tim Chin sees this post, he might have some advice as well. He seems to be pretty good at this stuff.
Get a service manual, and good luck. :-/