I believe you have a stuck TCC, meaning it won't disengage and hence its like braking a standard shift without pressing in on the clutch. The thumping I think is just the rear brakes having to work so hard, I remember mine made a noise like that once during some hard braking, hope this helps any, good luck.
I drain and replace the fluid at every other oil change, about 2.5 qts, it stays nice and fresh, maybe I change it to much but fluid is cheaper than transmissions.
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