Wow.
A new rider who doesn't immediately go to a loud exhaust or "I NEED a bigger bike! Thinking R6!" as the first things on the upgrade wish list?
Good advice above. Tires first. Then suspension.
Personally I never had a problem with the stock gearing. I like to say the party starts at about 9,000 rpm, and the bike will run all day long at those kinds of revs. I put 12k or so on mine, rode it like I stole it, and was never unhappy.
I did do clip-ons and rearset adapters on mine, but for ergonomic reasons. I found the more aggressive position more comfortable. That bike was never ridden on the track.