These things don't start out especially competent, but most things are easily improved upon.
Brakes: Change out the fluid to a good synthetic DOT 4 like Valvoline. Get some sintered (HH) brake pads on it... and when it needs rotors there are some good choices in lighter/better rotors as well.
Handling/suspension: Better than OEM tires is easy enough. The rear shock pre-load can be made a bit stiffer and some good fork oil like Amsoil 'Shock Therapy' 10W will also help. Since the bike is obviously limited in cornering clearance, you will learn to ride gentle arcs instead on sharp angles. You can't go in deep and late apex these things... you have to plan a more smooth and conservative line... but you can do better through a twisty section than people think.
Not much you can do about the trans... it's loud. You'll get used to it. Keep the shift linkage well lubed and the clutch cable ends well greased and change the oil often... that's about all you can do.
Performance: This is something you can have if you want it. A decent airbox like S&S/Lloydz or Torque tubes, a good 2-1 pipe, a timing wheel, and Power Commander w/dyno-tune will have it running exponentially better, stronger, cooler, and it can rev higher too. You can add cams, compression, inches, turbo, supercharger... The limits are Lloyd's imagination and your wallet. www.lloydz.com
Comfort: Nothing like a good seat, and the bars are easily changed if you want. I know it's hard to get used to the feet-forward thing for you... but it will feel natural after a while.
Good luck with your new toy.
2006 Victory Kingpin
Lloydz 116" Stroker/Big Bore, .495 Cams, Torque Tubes Airbox,
RPW Thor Pipe, Lloydz ECU Flash, PC-III, PTS (-2), Rivera
Primo Clutch Spring, 31 Tooth Pulley w/Buell Belt.