Pinion angle is about the angle of the u-joints on the drive shafts, has nothing to do with the yoke coming out of the trans case, that is dependant on the height you raise your vehicle and the length of the driveshaft and how much yoke it leaves in the trans case. When you llift you are basicly moving the rear axle away from the transfercase thus requiring either a longer yoke (they do make them but isn't the best way to go) or a longer drive shaft that telescopes like the front drive shaft does to make up for the change in distance from the transfer case to the rear end pinion. SYE does away with the yoke that currently slides in and out of the T-case on the end of the drive shaft, so now the yoke is stationary thus requiring the telescoping drive shaft, which generaly is bought with a CV style joint on one end to help elliminate the vibration that would be associated with the change in the pinion angles. By lowering your transfer case you have in essence made the distance between yoke and pinion shorter again. If you are worried about your slip yoke, jack the back of the jeep up via rear hitch or "frame rail" to let the rea suspension hang, mark the slip yoke wih marker, then pull the rear driveshaft and see how much length is still in the transfer case at the drooped suspension position as identified by your mark on the yoke, you should have at least roughly half the yokes length or better still in the output of the transfercase in full droop, if not, either put some sort of limiter straps on the rear to prevent it from drooping to far if your off-roading, get a longer yoke, or install a SYE, or of course the last and least interesting option, don't off-road it hard core, course that isn't why you lifted in the first place now is it. I don't really think you have anything to worry about if you get your rear lift compressed back down to 3"- 3 1/2" overall, right now your in the scary zone (your only 1/2" lower in back than mine) but like a suggested before, I would pull either the overload or the next one up, that would put you back in the safe zone, relitively speaking of course.
Pinion angles are what play into u-joint life and what create the harmonics you are feeling at highway speeds. That is why I told you you should be checking your pinion angles, also just checking them isn't all you need to do, once you get your measurements you'll know how many degrees you are from the more ideal angle of 3 degrees overall and that will let you know which spacers to get to shim the rear to the proper angle. The best link out of those was this one --->
http://www.steeda.com/-techtips/pinionangle.htm it really makes it clear what and how to measure whith the exception of what the use for the "level refrence" the drivetrain angle is what you should use for your "level" refrence IE the angle of the output shaft (or the centerline of the slip yoke which is what connects to the output shaft) not the floor or ground. It means you need to measure both the pinion angle and the yoke angle to get your overall u-joint angles, which is what it is all about. This other link is also good in the description of the how and why --->
http://www.buickperformance.com/Pinion.htm
As I have said, your vibration is/will be due to pinion angle because you have altered the ride height and the transfercase angle. Lowering the T case helped a little, but there is just a little more you need to do so that u don't explode a u-joint, trust me, thats no fun. Removing one of those leafs will also help this a bit too, thus the reason I keep mentioning it.
