Honestly, with that small of a difference I wouldn't devote any time to it. And if you just did the lift/etc, stuff is still going to settle for a couple of months anyway... so if you change stuff around and get it 'perfect' now; its probably going to be out in some other way by next spring. You may be able to influence how level the back-end looks by messing with the torsion bars up front as well. If you cranked each side exactly 6 turns, one may have actually lifted more than the other. But to get back to my original point, 1/4-1/2" difference on a 11 y/o vehicle when the suspension has been modified is not a big issue.

For 3" of lift, a one-piece driveshaft (OPDS) will save you a lot of headache down the road. Plenty of prior threads on this; and the price seems to have a large range depending on where you live. The frame crossmember doesn't need completely cut out for a OPDS; just parts of it. As for effects on the frame's structural integrity... all I know is that a lot of 'Zu owners have done it and wheeled hard for years afterward and I don't know of anyone's frame twisting into a pretzel.

In theory, if you add the same leaves to both sides of the back-end, you'll still have the same amount of difference only with a taller overall height. Of course in the real world the leaves may have a slightly different effect from side to side, especially used ones out of a junk yard, especially once they have a few months to settle into their new application.

With no more time/effort than it takes to undo the bj flip, I'd at least give it a try to see how things look before you take it in for an alignment. It may help and make the alignment process go more smoothly; or it may do too much and throw off the camber in the other direction.