Looks like you'll be splitting the lower cases as the broken gear is mounted to the uppermost lower case. It'll give you time to check around for the broken parts and any damage that may have been caused by it.It'll also give you a chance to clean any rust from the gears, check the action on the kickstart, check the shifting forks for wear , check all roller bearings and needle bearings at the end of the primary and other shafts, not to mention the overall condition of the primary drive chain and crank bearings. This is something you want to do once in this motor,so take your time and make it worthwhile. Don't forget the complete gasket set, shifter and kickstart seals too. If the two crank seals are bad and needs replace , the 550 at honda says NA but the 650 were the same and still available last year. Don't forget to blow out all of the oil passages both ways incase there is some pieces lodged in it. My thought is that a thorough clean up and inspection is in order just to be sure pieces won't damage anything else. Last thing since the top end is off.do you remember the condition of the camchain as you took it off? was it stretched? If so , now would be the best time to change that out too.
Clutch.... clean it up good, take any rust off the metal plates, soak new clutch plates in engine oil overnight before assembly, new springs wouldn't hurt either. then you know what you have.
Oh, before I forget , handling gears, for the first time, roll the entire shaft up and out,hold the entire shaft with one hand on each end, like a corn cob ,so it doesn't spin out of your hand and end up all over the floor. Sounds stupid right but, you'll be glad you did. That's it for my thoughts. Have fun.
