Here is exactly what is happening. You have 3 mounting points for the diff. 2 in the front and one gel filled one in the back. When your shifts aren't smooth enough, the front of the diff will move up and contact the rubber bushings in between the diff and the subframe. That is where the thump is coming from. You will figure out how to deal with this over time with the clutch and throttle input. It is really nasty when those bushings go out or are not put back in after a diff change.
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