trans, diff, flex discs, which is it
 

have a 1993 300E 2.8 and whenever I brake harder than just a gradual stop, the trans seems to thud into gear. If I hit the brakes and then give it gas again before the thud happens, it's like the trans isn't in gear and the car shakes and makes all of this horrible noise before finally shifting into gear (with a loud thud) and accelerating. I don't know if this is a trans, flex disc, or diff problem, but the thud and the other noises associated with this all come from the rear end of the car.

The trans has no other difficulties. Other than this, it shifts smooth and wonderful.

Any thoughts?

thuds
 

you might check the differential mount bushings in the rear. the left side is the one that usually goes first.

would that account for the violent shuddering that it does if i hit the gas before the thud?
I've also noticed that it seems to take a few extra seconds to shift into gear after i more the shifter from p to r or r to d.

that would be transmisson problems.

trans problem
 

your harsh shift is probably caused by lack of vacuum to the modulator,or rubber cap on mod is cracked,or mod is bad,or something critical is broken in the trans.hope for your sake that it's 1,2 or 3