I have a bad clunk when taking off. Always had it...mostly cold but it's not from the transition, it's from all the loose parts of the rear gear case..mostly the axle splines and carrier and the coupler link between the engine and gear case. All you can do while in your transition is ensure all bearings are play-free, that thrust washers are correct, that the gears and dogs are in good shape and that the full engagement of any gear position lines-up with the detents.