Even if the input shaft was damaged, it does not explain the low bite point of the clutch. If bite point was good and then changed then a clutch issue, if low from the get go again a clutch issue.
Perhaps part of the clutch failed and is fouling?
This may or may not have damaged the gearbox?
Silly question, did you remove the stud that holds the starter? That is a PITA and may have caused you to struggle getting the box home?
Did you changed the slave cylinder TP, I have seen these with incorrect pushrod length, this causes the thrust bearing to become dislodged?
Having listened to the noise again it does sound very much like a primary shaft bearing noise, but that is a large bearing and would have taken a lot if stick, spigot bearing dislodged may have allowed the shaft to run out but, again doed not explain low clutch bite point from first driving it.
I feel your pain, gearbox out again
That's all I can think of in the middle of the night with 'Wrath of God' like high winds waking me up!
Regards
Dave