If I remember correctly the screws for the fairing and cover are different lengths. If you used the same screws from the fairing, they may be too long and are causing the issues.
2010 696 ProTune Powermap programmer, EvoTech tail, Quat D Alum slip ons, Artrax wavy rotors, K&N, 14T, bar risers, G2 Throttle Tamer. Still working on swapping all of the black plastic over to carbon fiber. Oh, and no more ugly charcoal canister!