The best way to eliminate the clunk is to drive the car like you stole it.
Clunk/notch is substantially less apparent when shifting at 4K-4.5K RPMs and up.
Its like the car is complaining your driving like a grandpa. I know its hard to rip around everywhere you go, but it pretty much eliminates the clunk/notch of the driveline/trans.
My car has a ton of driveline noise when putt'n around parking lots or just mellow driving to the store and back.
Hit the M button, right foot to the floor=clunk/notch gone!!!
09' AW M3, 6MT, Black Novillo Extended, Carbon leather trim, Premium, Moonroof, OEM Carbon spoiler, BMW LED Int. Bulbs, Avant Garde 19x11/19x9.5 M310 wheels, OOLux V3 AEOO, Vorsteiner Type II diffuser, Megan Racing Stainless exhaust, Benvo Stage 1 tune, Dinan High Flow Carbon Fiber Intake, Dinan Front anti-sway bar, H&R Sport springs, 30% tint