I have to pull the transmission on my 07 to replace 2nd gear.
Would it be wise to use the 99-00 busa manual linked in the Maint. DIY section for pulling the trans?
You can use the 99-00 manual. There are only really small changes in the manuals. If it makes you feel better, you can download the updates for your year of busa.
Dont forget to get a lower gasket set, new head gasket, and maybe new piston rings. Its a good time to put in 2 intake cams and some high compression stock bore pistons too....if you have the extra money.