for my modest point of view and my experience, this is normal!
mine had HUGE problems with hesitation since i reached the 1000 miles, bike shutted off several times and i returned the bike such lots of times that the dealership wanted to give me the money back!
put some more miles on the bike and wait, see if gets better, i had huge improvement changing the pipe, air filter and open airbox.
but i gotta tell you that mine is doing it also now, after a year and 5000 miles, once in a while but is still doing it!
and i tried a friend of mine's one, older than mine and with more miles, and had exactly the same problem!
you bought a Buell, is not a normal bike, remember!
is just weird that they changed the fuel injection on the '08 models but they didn't fix this problem...
i don't think is the TPS cause is the first thing they do when they sell a new Buell, resetting the TPS!
could understand if you changed the ECU, but very rare if is a stock bike!