I'm always wary of shops being able to point to problems that I
couldn't see or hear. Know what I mean?  ;)

If the link bushings and stabilizer bar didn't make noises before, I
don't see why they should right afterwards. Sounds like they've
probably forgot to tighten something in the process or didn't put back
the rubber spring seats in order to cause clunks. The strut mounts
could have gone bad as well when they take off/put on the strut nut.
Toyota mounts aren't the best so they also may have simply crapped out
as the rubber come unglued from the metal housing.

KYB struts are nicknamed: "Keep Your Bilsteins" in the tuner circle.
I'd actually avoid KYBs. Gabriels (like Monroe) make different grades
of shocks and struts, my premium Gabriel Ultras are great. Check out
their G-force inertia sensitive valving video:

http://www.gabriel.com/gforce1/eng/default.htm