1)You prob should read up about jetting the bike, your open throttle bog could be from too much fuel (may need to drop jetting).
2)You would most likely need to order those bolts Yamaha dealer IMO.
3) I don't know much about carbs but depending on what kind of riding your doing the head and pipes are nice. I personally run CPI pipes and a F.A.S.T Racing Noss head and stock carbs.
4) As for maintenance changing fuel like you already did, new plugs and clean your air filters, and change your gear oil you should be ready to rock out!
I don't know much about that honda oil??? (i run Amsoil Interceptor in my 06 banshee)
I'm no banshee expert, but just my opinion on this stuff.