I originally posted this in the Engines/Drivetrain forum and ran out of steam. I thought I'd try here.
I have a shudder in the car, and I can't tell if it's in the drivetrain or the engine.
Does anyone know a good way to troubleshoot this? I really notice it if I stall up to somewhere around 2000 RPM.

I've seen something a little similar to what you are describing with rotted rubber engine mounts that had split. Worth checking anyway.

If the visual inspection of the mounts turns up a dead end here is another idea. There was a guy here a few months back with a similar problem. He removed the transmission and blocked up the rear of the motor (watch that distributor). He then discovered the vibration was comming from the motor. In fact, his crank was out of balance. Just remember when blocking the motor, het it secured good. A floor jack and two by four could lead to disaster if it falls loose when you rev it up. It might be possible to remove the converter bolts and slide the converter away from the flex plate enough to get it out of the pilot bushing. If that will work, it would be far safer and easier. This wouldn't be a good idea if the pilot bushing doesn't disengage.

-dnult