part throttle shifts are tough but you can learn how to make them not clunk. have to learn to sort of feather the throttle at the right time.
are you part throttle when this is happening? I've found, while part throttle, you sort of have to sense when it's going to shift and back off the pedal a little just before that.
are the requested torque tables (I think these are the ones, utc_pyro [i think] might know better... the ones that have to do with injector pulse width) updated in your tune if your injectors are larger? it helps the TCU know better what the real requested torque is and might have an impact.