Hey! Welcome aboard and congratulations on the new purchase. Was this the bike on Craigslist in Indiana maybe a month ago?
The transmission upgrade is the biggest deal, followed by remapping the computer. Fortunately, the transmission is a cassette design and can be removed in an hour or two. There are detailed instructions in the Tech section.
Atlantic Excelsior-Henderson is our parts go-to. Marty and Jamie can set you up with all the parts you'll need. They also have a machine shop they deal with that does the machining of new bearings for the gears. You remove the cassette, ship it to them, they do the work and ship it back to you all done, with spiral circlips installed.
They also offer the latest fuel mapping for your fuel injection: remove it and ship it to them. The reason behind the fuel mapping is both running quality and engine temperatures. Things tend to run pretty hot with the original tune and if you crack a cylinder head, it's very (VERY) expensive or impossible to fix. This importance here really depends on how you intend to ride the bike.
http://stores.superxparts.com/