Dexter part of the suspension being stiffer is most likey parts binding. The more you lift it the more things get stiff
Not installing a raised bracket in the rear makes a TJ shake its tail quite a bit more than when you try to get the trackbar close to horizontal at ride height. It does make a big difference in ride quality, I chucked the bracket originally and raised it up later made a big difference. I know its tough on the left upper control arm bracket that's why they break I braced mine pretty well when I raised the trackbar up. Ultimately a 3 or 4 link will make the back end happy, it will get rid of the trackbar action and allows much better flex in the rear and greatly reduces swaying side to side of the body combined with some decent offroad sway bars.
Now back to the original problem the stock springs have arubber pad on top which is now replaced by a piece of urethane, this will make it a little harder, you changed the angle of the control arms a bit doesn't help it either.
The part you can control is binding of the trackbar, if need be look what the right height is then take the springs out, set it with a jack at ride height and try to move things around also did you do anything about shock lenght?
For centering inside tire to frame in front and inside tire to spring bucket works well. One last thing Loosen and then retighten the control arm bolts when the supension is loaded with the wheels on the ground, loosen the bolts bounce the suspension then tighten, that might help some and the bushings will live a lot longer