Changing your shocks should help with the rear end sag and / \ arrangement of the wheels. The rubber boots over the constant velocity joints in the rear axles are pretty rugged. The exterior can look a little worse for wear, but if they still seal the grease inside, and keep the dirt and water on the road outside they are as functional as they can be. If grease is leaking it is apparent. 100k miles is not an identified endurance limit and changing the boots is an ordeal, so I would tend to leave it alone until you see leakage.
If you don't know when the differential fluid was last changed, and you go through the trouble to check the level, just change it. It can only help.
Clunking can be from a variety of things, and I guess I can't point to anything in particular. Hope this helps, and good luck, Jim
1986 Euro 190E 2.3-16 (291,000 miles),
1998 E300D TurboDiesel, 231,000 miles -purchased with 45,000,
1988 300E 5-speed 252,000 miles,
1983 240D 4-speed, purchased w/136,000, now with 222,000 miles.
2009 ML320CDI Bluetec, 89,000 miles
1971 220D (250,000 miles plus, sold to father-in-law),
1975 240D (245,000 miles - died of body rot),
1991 350SD (176,560 miles, weakest Benz I have owned),
1999 C230 Sport (45,400 miles),
1982 240D (321,000 miles, put to sleep)