You might try pulling the flywheel cover off to make sure it is not the bolts rubbing on the case. This is not that hard of a job to do. Try to rule out the easy fixes first before going into the tranny.
2003 Polaris Predator w/K&N filter, HMF pipe, Pro Armor nerfs, tether kill switch, PRM Baja bumper, PRM skids plates, Hiper rims, Kenda tires, Renthal bars with Spider grips, cycra handguards.
1999 400 EX Stage 1 Hot Cams, K&N with air box mod, PC t-4, LSR 2+ axle, Holeshots all around, Prm bumper and skid plates, Pro Design kill switch, Rental bars and grips.