In addition to the flex couplings, the rear drive shaft leading from the rear diff to the tyres can also wear to give that clonk.
A worn trannie can cause all the above, and if that is the underlying problem it may be best to fix the transmission before doing the rest.
Been there with my autobox and ended up with a trannie overhaul before I eliminated the problem.
Hope this helps.
1983 w126 280SE - daily drive
1983 w123 200 - sold