do you still have the original shift modulator in there? could be about time to change that ($11 cant hurt), but it sounds to me like your tranny mounts are weak causing the thud. fill them with urethane.
btw, i notice my car will do the same thing if i am going at a speed (like 35) where the trans tries to double downshift (i have skip shifts thanks to tony), but it just revs in N then slams into first resulting in barking of the tires, a hard shift, and my head hitting the headrest. not good for the tranny at all, and it mostly happens when it is too hot. i try very hard not to let this happen.
b/c the 96's are vac controlled it may just be that our cars gets confused more easily. since it is manually adjusting the pressure on vacuum instead of being exactly based on tps and pcm values. sometimes cars just do wierd things, but if you notice it happening more often then report back.
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1996 with 254k miles, L32 4" FWI -> ported N* -> Ported Gen V w/3.0" Pulley, Stage 3 Phenolic I/C, ZZP FMHE, 1.84 RR, Headers and 3" pipe to mufflers, F-body brakes, and lowered on Eibachs. -RIP
AMG C400 White on black. Stage 2 w/E30 - 11.9@117 -daily