Don't sweat it, it's not time to put the ol'Roadie out to pasture just yet.
To sum up what's already been said:
Step 1) Remove the lowers and let the engine breath!
Step 2) Get some adhesive heat shield [sheets or tape] and put it on the bottom of your gas tank.
Step 3) Do a "system shock treatment" with either Seafoam [as described on Curt's site] or Yamalube Ringfree to remove carbon build up!
Step 4) Dial in your carb
[read the articles in the tech section to learn how.]
Step 5) If problem persists, remove the fuel pump.
Step 6) Add some Seafoam or Marvel Mystery Oil to the gas tank every couple of fill ups to keep system clean.
Step 7) Ride'r hard every once in a while when she's good and hot, hitting the rev
limiter briefly to prevent carbon build up.
Step 8) Enjoy another 50K+ miles on the bike.