Had the same problem with my 06 1200r only 2nd gear and the run around began.
The reason BMW doesnt sell individual gears is because by the time they got done reworking that transmission when they stopped making the bike the trans components were no longer backwards compatible with the old trans. My understanding is that the gear dogs were straight cut and under the monster torque of these bikes they can round and hence the slipping out of gear we are experiencing,.
I lucked out and found a used trans with 5,000miles on it and jsut did a straight swap.
The option i was looking at before that fell into my lap was going to be to remove the trans and send it off to a trans shop to have the gear dogs welded/undercut. That was going to be about $500-$1000 USD with the purchase of the appropriate new shifter forks(still compatible with old trans to my knowledge).
Moving forward if you cant find a replacement trans i would sent out the current one to be modified and replace the shifter forks that are affected while your at it.
Definitly buy the reprom manual and the clutch basket wrench(75$)(Ask me why i know to buy this haha) because the clutch nut is torqued on there at 200 nm and it is a mother to get off. Also recommend using a electric or pnumo impact to remove that because it is a bear!
IF you have any questions let me know!