MY 99 YZF-R1
These are the only changes that I have made to my 99 R1. As you can see I have not done much.....the bike is pretty amazing out of the crate. Complaints (minor) - Mirrors (great view of shoulders), windblast (seems to hit me right in the visor in the normal riding position), seat comfort, Tank shape (even a shapeshifter wouldn't be comfortable laying on this thing !). 

o Superbike Grips - Increased comfort, reduced buzz

o Lockhart Euro Dark Smoke Speedscreen - Better than stock, but not much

o LP Carbon look tank pad