A liitle help, please

I posted this over in Driveline Discussions and I'm not getting any info so hopefully the change in venue will get me some answers.

I've got a 2007 4x4 NISMO with 120k on her(i've put 2k on it myself), here's the issue.

Went out to a offroad park on Saturday, no wheeling just checking it out, I hit a rut on my way out at about 10mph, bounced my head off the headliner. Driving home I noticed when the truck downshifted, 4th to 3rd, 3rd to 2nd I would get a intermittent thump/clunk. It did this all the way back to work, I tried driving with o/d off and that seemed to help. When I drove home, after the truck cooled of it didn't do it anymore, so I thought the tranny was having a brain fart. I drove to and from work on Monday with clunks, I live 5 miles from work. Tuesday I took the truck to town (12 miles) it started clunking on downshift sometimes, and studdering on upshift. took the truck to dinner last night, it started clucking on the way home. Any ideas on why its doing this and only when hot? The only mod to the truck is I have flashed the ecu with the xs gas saver superchips tune. I currently have it in the shop having the tranny flushed and filled, and getting her checked out underneath making sure I didn't break anything.

Thanks, hoki