Mine is lifted the same way, have both of those problems.
When you crank your front end up, the a-arms have less distance away from each other
In the sway bar end link area.
I bought my truck this way and when I rebuilt the front suspension and steering I flipped the end links so the threaded end faces downward.
As for the rear, I assume its a number of things causing the jerk/squeek.
One, your leaf spring had a lot more torque-twist on take off caused by moving the axle 3" away from the leaf.
Two, you loose about 1.5" of spline coverage on your transfer case yolk.
Add those two together and you aquire some problems.
Something you haven't looked at yet is the upper balljoint bolts (if it has had them replaced before, if not it won't be long).
The angle causes them to dig into the steering knuckle and this eats the bolt away.
I noticed this on mine searching for slack.
If you want three inches, despite the pros and cons they have, a body lift is a better way to do it.
Upon my next rebuild I will go back to stock suspension and a body lift, have some used oem u-bolts aleady just missing two washers
Body lift is more labor intensive than what you have done, but it saves lots of $$$ in both the short and long run.
