before pulling stuff off are you doubly triply sure the brakes are bled all the way especially the front end?
With dual system brakes, you may have pedal pressure giving you rear brakes and rear brake lockup, but still have air in the front. Was the MC pre-bled before install?
sorry if you have done all this, but usually these things are a result of the easy problems vice some bad cylinders or bypass or residual valving.