By using longer shackles you changed the bend of the rear spring which in turn made the pinion driveshaft yoke tilt upwards.This changed the angle which as you said you already know must match the driveshaft yoke angle on the transfer case.You have to measure the angle of the yoke on the transfer case ,then measure the angle of the yoke on the rear diff.You're going to probably find a 6 degree difference with a 3 inch lift.Many off road parts companies sell angled shims to put between the rear diff spring perches and the spring under the U bolts.This will tilt the rear diff which then should be the same angle as the transfer case yoke.Like someone already mentioned you can get a cheap angle gauge from harbor freight or possibly home depot.If you don't get those angles to match or at least be within 1 degree you are going to get vibration and blew up u joints.
This is one of the cheaper easier ways to correct your problem the others mentioned are also very good but more costly.I don't think a set of shims will cost you 30.00

CATFISH