Sorry to hear you are having problems but this problem sounds very familiar with myself and other Vee owners. I had this issue when I purchased my Vee and did everything to try and resolve it, I'm not sure why but after checking everything on a completly stock machine I couldn't understand how it ran like that and eventually drew a blank....
but in the end I gave in and bought a power commander III which ironed out all running issues.
I'm not sure if your Vee is the same but mine is super sensitive to crap fuel, have you tried a fresh tank of fuel..? maybe higher octaine ..?