@linjam, hang in there and try not to give in to anxiety. I've been there - my transmission was rebuild 3 times over last 5 years/ 20k mi.
From my
personal experience, the source of clunk that I think you are describing is transmission itself. Before my 3rd/last rebuild, that was done under warranty about a year after 2nd rebuild, transmission shop tried adjusting pressure 3 times - from very firm, to less firm, to even less firm, to eliminate my clunk/jerk to no avail. After they opened transmission they found "some issue with a clutch pack". That's just 9-12 months and less than 10k mi after it was replaced with new parts.
Right away after 2nd rebuild I had a vibration issue that was resolved with a new driveshaft center bearing. It might have gotten damaged somehow during transmission R&R. New flex discs were put in at the same time, although they weren't bad, just a few micro cracks. So, I think, I can differentiate transmission clunk from driveshaft bearing problem. After 3rd rebuild - I got my car back about 1.5-2 months ago - clunking was gone, so I know it was transmission itself. I'm still keeping my fingers crossed. Should have bought a remanufactured transmission directly from MB the very first time, but, oh well. This is my specific experience and I hope it's not relevant to your case.
You say the shop that installed the transmission for you is experienced, so they must have connected everything correctly, and inspected vacuum lines that connect to it and everything checked out, right? Sun Valley must have done their due diligence as well, as far as pressure modulator, etc. If your flex disks were apparently bad, the shop would have noticed?!
Let's hope adjusting pressure will resolve the clunk or that installing shop made some mistake, by not connecting something correctly.