This has always been pretty normal for my VX. Even after I lube up the joints and check over all drivetrain elements. Solid as can be. It's a clunk that comes and goes. I notice it more when the VX has been in Park on an incline. My impression is, expect SOME clunk, as this tranny is pretty solid and tends to do that. It *IS* a truck afterall. You should keep all joining members well lubed up to keep the clunk at a minimum though.
Having the rear end replaced could lend another set of issues though. If the clunk is more apparent after the work has been done. I would take it right back to the shop that did the work. And dont settle for some undercover *we dont want to work on it* excuse, heh.
Gary Noonan
'01 S/C VX / '18 Forester XT