As far as not marking the tailshaft where it bolts the diff flange, not really necessary as you said it sits on the flange shoulder, the shudder you get, is it as you are releasing the clutch as in could it be really bad clutch shudder or is the clutch fully engaged when you feel the shudder ??? if its also there when the clutch is fully engaged & your foot off the clutch as you are aware you have some issues, I would suggest a seized tailshaft uni or something really badly out of alignment & way way out ..
With the back end of the car jacked up get under there & turn the tailshaft around by hand & see what its doing & if you feel brave chock the car well & with the back end still raised get someone inside the car to start the car & select a gear & slowly engage the clutch whilst you are under the car & see whats happening, you will probably see the fault then, but do so at your own peril ( you lost me in your description of the bearing tightened up a little when I fitted the plate back onto the tailshaft )
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