It will probably always clunk but it gets quieter. In the mean time try to preload your shifter on upshifts by hold pressure on it before you pull in the clutch. Also don't lug the bike and try shifting between 2800-3000 rpm.
Retired USAF, IYAAYAS!
2008 V-Star 1100 Custom Bobber project
2011 Crimson XR with Forged Highway Bars / Hard Bags / Passenger Backrest, Ness parts including Smooth Layback Plate Frame/Mount / Rad 3 Mirror / deep cut grips / drivers floorboards /shifter peg / brake peg / passenger pegs. Witchdoctor black rack, Lloydz filter / timing wheel / VFC III, 7Jurock windshield, Drag Specialties seat.