Vibration and Noise Issue

Your problem is with the shaft..
The only way your pinion can make a issue is if you can physically move it.

I've seen a bad pinion bearing cause a vibration and not have any movement. It had a flat spot on a roller. Changed the bearing and race and the vibration was gone.

Changing joints can throw a shaft out of balance, putting the slip yoke on opposite of the way it was balanced with the shaft will make a vibration.
Dropping some driveshafts can and does knock them out and need to be balanced.

I agree dropping a driveshaft can definitely mess it up but no way is putting the yoke on backwards going to throw it out of balance. The driveshaft is balanced independent of the yoke.

The screwdriver method in the car isn't perfect since there is some movement at the slip and your arm is not a fixture, I don't care how still you think your arm is... No good..

Angles directly effect load and unload and rpm.

If your angle is way out you'll have a load vibration, or a decel vibration.
If you exceed the rpm for the angle of the joint it'll progressively get worse or burn the joint up and vibrate.

I agree if the pinion angle is off it can introduce a vibration

You either never realized the vibration or just ignored it or got lucky..
I'll go with you ignored or didn't realize that noise, hum, buzz was the joints you changed..
Not all vibrations are physical to feel.
Every part of a shaft is balanced as it sits, so if you do not index the parts of the shaft as it is, it'll have a balance issue.
Just changing joints can throw a shaft out..
I see it a lot, very rarely do people get it right.

I can't agree with you. I am very aware of even the smallest of vibrations and I especially don't ignore vibrations or any odd noises for that matter. Been a mechanic for nearly 30 yrs. now. Don't claim to be the best but I have had a ton of experience with drivetrains. As I said above I do not agree the driveshaft is balanced with the yoke attached. A buddy and me just had to shorten his driveshaft for a trans. swap we did in his truck and they didn't balance the yoke and driveshaft as an assy. Just the driveshaft. That's how all the shops I've dealt with did it. I have seen people leave off the inside C-clips which center the U-joint and that'll cause a vibration but it's not really all that common in my neck of the woods.