Have you tried driving in front wheel drive only yet? Pull the rear shaft off, lock the hubs, stick it in 4-high and see if it's completely gone or not. I'm sure it will be, since you seem to have isolated it to the rear shaft, but it never hurts to get a confirmation so that you're not chasing your tail between two separate sources.
Since you say that messing with it has changed the way it vibrates though, you're at least on the right track. What about pulling the caps off of the joints to make sure that the needles are all in place and in good shape. Maybe add some more grease to the centering ball in the CV yoke too. Sometimes that female zerk is finicky and you might not have gotten enough grease in there the first time to keep it happy.
Just a couple of thoughts. Long-shots as always, but you never can tell.
Paul