Everything has gone wrong with my drivetrain.

[Bardiya]

My transmission was replaced last year and ever since then, I've had the P to D/R shift shock, extreme vibrations that come and go starting from 40kph and get even worse when I let off the gas.
I can feel the vibrations from the floor and through the steering wheel, it's strong enough to shake the rear mirror.
I also have a loud whining sound coming from the rear which might be related.
I've already physically inspected all U-joints (replaced one that had massive play but still made no difference)
Front, Rear, and transfer case fluid replaced.
My car is part-time 4WD but the hubs do not disconnect.

Has anyone been through this nightmare?

 

[KC100series]

I had a similar vibration and it ended up being a drive shaft. It might be worth your while to pull the rear shaft and take a drive with just the front in. Then do the same with just the rear in. That way you could at least definitively cross drive shafts off of your list if it doesn't remedy your issues

 

[UltraFJ40]

I had a similar vibration and it ended up being a drive shaft. It might be worth your while to pull the rear shaft and take a drive with just the front in. Then do the same with just the rear in. That way you could at least definitively cross drive shafts off of your list if it doesn't remedy your issues

That's good advice, at least you can narrow it down that way.