hey thanx for all the help guys, One thing i did notice when i removed the rear shaft, was the yoke at the t-case out put shaft doesnt look seated, properly, the nut is tight, but the seal is leaking and it doesnt look square.
When you spin the out put shaft you can see a gap in the seal when it spins only on one side, like its out of round. The nut isnt completely threaded on either. i could see abouth 5 threads on the nut? Probably the problem. O and no I am still running the stock skid plate.
If that is the case, your vibes should be a lot more pronounced then they are, but it does sound like your problem.
To fix it
Remove the dampener
Remove speedometer tone ring sensor (small torx, top of tailshaft housing)
Remove tailshaft housing (6 x 13mm bolts)
Remove the tone ring. 8 inch 2 jaw puller will work if its jammed up a bit. May have to jar it with a pry bar a few times to get enough slack to fit the puller jaws on
Inspect the tone ring pin seat, and the tone ring pin (new tone ring is 90$ from the dealer, about a 4 day order)
You can make a new, tighter fitting pin by cutting off the end of a drill bit. Test them in the shaft till you get the right size
Red, or green loctite the new pin and install
Coat the base of the output shaft (where the tone ring rides) in red or green loctite
Pre heat (oven or deep fryer) tone ring to about 160F for easy install and to allow loctite to get between ring and shaft
Wipe oil from the ring if pre heated in a deep fryer and quickly slide it into place on the output shaft.
Ensure ring is seated in its pin.
Let the loctite set up for at least an hour, or until you can not wiggle or slide the ring by hand.
Clean up tailshaft housing, mounting surface on the t-case, and re install with a small bead of RTV
Re install speedo sensor
Re install flange 185-250ft lbs (double check that, its from memory)
Top up the t-case fluid.
This is a pretty common problem on rubi's from the factory. The tolerance on the tone ring, and small size of the pin can allow the ring to shift out of its seat when pulling, or re installing a flange.
hope that helps