AFAIK, no there is not one complete bearing set. Just the crank bearing set like you have mentioned. If you have not removed your bearings yet from the cases, do that and get the identification numbers off the bearings and goto your local bearing shop to order them, they will be much cheaper than if you went thru Yamaha direct. BUT, if all else fails, order them online, MotorSportsSuperCenter Yamaha Suzuki Polaris SeaDoo CanAm Spyder Discount Parts Accessories has excellent prices on all OEM parts.
There is not they are all seperate. I had all part numers listed somewhere, I was able to get all of my bearings from cheap cycle parts.com you can also go to Napa, and they will cross reference the bearing numbers.