I bought a very similar XC90 a couple months ago. Same color, but my leather is black, my windows are tinted (not the drivers/passenger sides), and I bought it with 95k.
I also did upper/lower mounts, changed the stabilizer bar bushings, oil/filter. I also was having a clunk when coming to stop, it was very soft. It took me a week to get my wife to notice it. I could also feel it when accelerating, and when releasing/pressing the gas at low speed. It only happened when the car was warm, and it didn't happen on very very cold days (below 20). As it happened only when the car was warm, and it felt like a rough up/downshift, I thought it was the transmission fluid. I flushed with Toyota T-IV (same as JWS3309 but a lot cheaper), but nothing changed. After quite a bit of researching, I found the cause was the axle bolt getting loose. Re-torqued it and the clunk is gone. On S60s this is pretty common and the solution is to use XC90 axle bolts. Curiously enough, my XC90 didn't have the XC90 style axle bolts. Maybe they came out with the fix after my model year. I bought the new style bolts, but hadn't installed them yet. Anyway, it is worth checking, takes 5 minutes. Search for axle ping and there is quite a bit of information on S60s.