A few more questions?  
1.  Did you add a T-case drop kit?  or did you put on a SYE?  Anything over 2" requires one or the other.
2.  Are these new or used springs?  Which Brand?
Check out this link for Drive shaft angles:
http://www.4xshaft.com/index.html-For a 4" lift with a SYE/CV drive shaft you will need a 6 deg shim
-For a 4" lift with stock drive shaft and a T-case drop kit you will need a 4 deg shim
-For a 2.5" lift with SYE/CV drive shaft you will need a 4 deg shim
-For a 2.5 lift with stock drive shaft and T-case drop you will need a 2.5 deg shim
I put a 2.5" lift on my Bro-in-law's YJ and at first it sat about 3.5-4 inches but settled to 2.75" after the first time we flexed it.  He has the Rubicon Express (not XD) so it was a good kit.  I would expect your springs to settle.  My 4.5" lift sat at 5" for about 6 months but now is at 4.5 front and 4 1/4 rear (mostly due to the diameter of the 8.

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