As to the clunk,
check the tailhouse very carefully for external signs of shinyness, which would indicate it was hitting something.
As to the whine
Is it also whining in direct 4th gear? That would be unusual, unless the TO bearing is dragging on the pp, Or the front bearing is laterally loaded or worn out; because in direct the power goes straight thru the box.
As to vibration
Check the yoke index on your new driveshaft.
If you like, you can ship that box to me and I will get to the bottom of the whine. I won't say I can fix it, but I can tell you what is causing it.
I have many many years experience, decades even, in driveline rebuilding.
I need a pair of nice rear quarters for my 68 Barracuda, and some trunk extensions,lol
