I have engine vibration probs since day 1 of purchase. Now, a second air filter mounting bracket is busted, both times the mount point closest the firewall has broken off.
On top of that, the car vibrates at 40 mph and over, usually rythmically, to say the least, it feels like the vibrations are corresponding to how the cylanders fire, so I am pretty sure its a mount, shock or both.

How can I determine which is which and what I need to replace?

You would be miles ahead of yourself to just do both. I think it would be nearly impossible to isolate any vibration to just one or the other, and a failed motor mount will wreck a shock fairly quickly.

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1989 300E 144K

There are three components -

1.) Engine Mounts
2.) Engine Shocks
3.) Engine Shock mounts

Vibration, especially at idle indicates the engine mounts. A big shake before shutting down the engine indicates the engine shocks or shock mounts.

I pulled out the shotgun and replaced them all while I was in there, and what an improvement!

DieselGiant has a very good video showing exactly how to replace the mounts, it helped me a lot. A helper and lots of ratchet extensions helps quite a bit with replacing the shock mounts.

-dd

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'85 300D, 'Lance',250k, ... winter beater (100k on franken-Frybrid 3 Valve Kit)
'82 300D, 'Tex', 228k body / 170k engine ... summer car
'83 300TD Cali Wagon 210k, wife's car