i think quarkz is using the 03/04 subframe b/c the mounting points for the fairings etc are different. that would be your biggest issue i think. and mounting the taillights. i think she had to do some customizing to the subframe for it to fit the 02 frame. it's just 4 bolt holes that have to line up, but i dont think they do without customizing. i could be wrong about that...?
you need to adjust your stock suspension some i think. it offers a pretty good range of adjustability for street riding, imo. there arent going to be a lot of products for sport bikes that are aimed at giving a smoother ride.
i think the user 'vbroom' has hids...give him a yell. though, the 00-02 headlights are freakin bright in stock form.
i personally like the white/black color scheme, but it's very subjective. to do your frame properly you need to powdercoat it, and that will require taking the frame off the bike, which means taking the bike off the frame. including the engine and errthing. you can definately do it, im just saying its a lot more work than popping off the fairing and getting them painted.
a good sprocket size is -1 (front) and +2 (rear) from the stock sizes. that's kind of the standard change from stock, and it will make it easier to wheelie but won't lose a lot of top end.
pazzos are legit levers, and also check out ian's new
levers. look in the site vendor forum for info.
as far as brake lines, i'd go with some galfers, but i dont have experience with them.
i wouldnt shorten the pipe. it's your body you do what you want, though.
newer model wheels could be cool, just make sure they fit properly. they may require a spacer or something, and i know the rotor size has changed some years, but do your research and you can find out what all is needed.