[hybrid]

silent R1 you are correct, unfortunately I have no prize for you.

This sound most definetly like a 2nd gear problem, those are exactly the simptoms encountered. It will feel like its hopping teeth on the chain when in fact it is hopping dog to dog on the gear.

Take the bike and pull out in first and short shift into second at a low speed and smack the throttle wide open. This will load the motor and consequently the transmission it will jump if the dogs are rounded. Then stick it in third and the problem wont happen.

If it happens once in a while it is just now becoming damaged, but in time it will be all the time because it wont fix it self and the only fix is to replace the gears, shift fork and the shift drum involved. Most people will try to just put the fork in there to fix it but I promise its a temporary fix at best.

Silent.... the R1 has had notorious problems with the second gear, My recommendation is for you to remove the tranny and send it out to R&D TRANSMISSIONS and have him weld it up and undercut it. You'll find out from Mark the guy that owns it how bad the design is, they can only undercut one side of the shift pattern either up or down but not both because Yamaha decided to lose some weight from there and made the gears thinner making it impossible to cut up and down. If you get the tranny out I can save you some money on the service as I am a dealer for their services. I still recommend other thing depending on the year R1 you have