Actually here is an interesting part of the story.
While I was under the jeep cursing it's name, I had the transfer case in neutral and was slowly spinning the rear output shaft to see if I can hear any bearing noises (I didn't hear any noises). I DID, however, notice that the harmonic balancer on the output shaft is wobbling around like a drunk sailor.
This part, only found on some newer XJ's and most newer TJ's, has around 1/2" to 3/4" runout when spun slowly, I can't imagine it came like this from the factory and it's demise may have simply come at the same time as the lift. I noticed the rubber is cracked in a few spots which lead me to take a closer look and notice the runout.
The head scratcher (and I'm no engineer so this might be simple for someone else) is that with the rear DS pulled and running in "front wheel drive", there is no vibration at all. With the rear driveshaft in, I am getting terrible, rattle my teeth type vibrations above 35mph. If the bad harmonic dampener is to blame, why is it only showing up with the rear DS in since the dampener is spinning even in "front wheel" drive? Amplified through the rear DS? I don't know what the term for that is.
I also re-measured to see how much spline engagement I actually have on the stock slip yoke and was surprised to see that I am still getting 2.5" of engagement at static ride height. I figure that at most I have only pulled the stock slip yoke out approx 3/8" more than it was sitting before the lift and it's not, in fact, dangling off the back like I thought before. I cleaned up the splines on both the output shaft and inside of the slip yoke and ran my fingernail along them to feel for deformations I couldn't see with my eyes and I can't feel a damn thing. With the slip yoke engaged 2.5" like it sits at static height I can't feel any play between the slip yoke and output shaft, only if I pull it most of the way out and only leave 1/2" spline engagement.
For those not familiar with the harmonic dampener I'm talking about, this is what it looks like (photo I found online):