DON'T PANIC!
Ok, worst case scenario goes like this. Second gear, give it a handful, hit a bump, huge clattering sound from the gearbox. No drive in second.
That's what happened to me at 45000. I had the bike trailered back home, whipped the engine out and took the sump pan off. Second gear was missing a number of teeth. Now, about 10,000 miles earlier, I'd missed a gear on a track day and when it went back in, it made the most almighty bang and I'd always wondered what that did to the box. Turns out, it was probably knocking seven colours out of second gear. Having said that, it was always slipping out of second, and from what I hear Yamaha R1 gearboxes are also prone to this as well. Known problem.
I'll bet this isn't what you want hear .. . .
Anyway, stripping the whole thing down and replacing that one gear was way more expensive that getting a second hand engine unit, so that's what I did. Took a couple of days to swap the two units, but this replacement has never slipped out of gear and I'm up at 91,000 miles now. I see on eBay tonight, there's one for £330. Way cheaper than getting dealer to strip the engine.
I hope it's not as serious as this. I really do, but if it is, don't panic, it can be rectified.