I'd be curious what else was removed from this moto, besides the fairings..... If it's supposed to be an RT, someone has done some modifications on it.
As Laitch has suggested, I'd be checking the fuel filter 1st, then I'd suggest getting some techron FI cleaner and run some of that thru a couple of tankfuls of gas.
After you do that, if it's still acting up, we can go deeper.