Now since it only has 25,000 miles on it I doubt this is it but if the previous owner installed Tone's interceptor (intercepts transmission electronics) they could have the line pressure set high and that would cause a pretty good clunk, but mainly during downshifts.
However I get a lot of clunks with mine as well, and it could possibly be normal...... maybe make sure your drivelines are solid as well, grease the zerks. Keep your eye on the dash lights to see if the light jumps around from "2nd" to "D" to "3rd" etc. this seems to be the real tell tale sign that your mode selector is out of whack.
2001 Ironman Daily Driver... 3.5" suspension lift (OME912 springs and 1" spring spacer), ball joint flip, 1.5" front diff. drop, 33"x12.5 TrXus MT, 16x10 Eagle Alloy rims, Interceptor, PV muffler, K&N air filter, Alpine Supercharger, Bilstein shocks, and some trimming.
2000 Ironman Project LS-1 VX... very slow progress but someday....... ohhhhh someday......