Following. I have the same symptoms. Thinking of pulling it all apart tomorrow. Hope its simple, like a pilot bearing in my case.
How does one properly measure end play in the input shaft? Also, no one answered his question about how it could be the input shaft if the input shaft is stationary while getting the vibration, i.e. clutch pedal pressed, trans in gear. So, the input is not spinning, nor is the clutch disk, and if the snout is in the pilot, I don't understand how it would be the source of what feels like a balance problem.
If I go in that far, and I find myself in your shoes, without any obvious clue, I'm taking my stuff to a mchinist to check the balance.
If the pilot bearing is off center or egg shaped, the input shaft will not spin concentrically. Once you remove the input shaft from the equation, the pilot bearing has nothing to spin elliptically to give those vibrations.
As for measuring end play you'll need a dial indicator, an indicator stand, and some way to secure the transmission to ensure it doesn't move while you physically push/pull the input shaft while watching the indicator. Without having specs in front of me, I'd suspect that you don't want more than .001-.003 fore/aft movement.
(Just found this short video - apparently it's .001-.005)
View: https://youtu.be/hpd4IBpLk8o?si=X_duFbbqV5jGwVq9