Slight movement of the input shaft would not disturb me as the front of the shaft is supported by the pilot bearing in the end of the crank. If by manipulation you find that all the gears seem intact install it.

To knock the tranmsission down will not prove all that much anyways in ny opinion. For example if a syncro had a bit of wear it is hard to tell if it is too much. They can be a little deceptive.

The really saving grace is these transmissions were designed to handle much more horsepower than our diesels put out so they are durable in service usually. Sure a few fail in some way or another but the odds are with you it is still okay.
Another thing I would consider. Did the car look like the milage was real or more like a 500k example? The bulk of these older mercedes do not have accurate indicating odometers but some do. Try to get a feel for the car. Sometimes with a little luck the last owner can be found to question.