A little update... been a year since the rebuild now. She's running great, and the paint still looks new. There are a few spots where I can see rust staining the white paint in a seam here and there, but nothing major.
I added a Summit Racing CDI ignition and now get consistant 15mpg according to my GPS. Not bad for a 30 year old 258 and 3 speed auto running 3.54's and 31's (and considering I was get about 12 mpg before).
The shackle reversal is fantastic! I don't do much offroading as she is mostly my weekend run-around vehicle. I can't believe how well she rides with the springs reversed... two thumbs up.
I still dislike the look of the YJ cage, but feel a lot better about running around with the kids in the back when they have the benefit of the shoulder belts. One day I'd like to get some of those sport-bars that bolt to the dash.
'80 CJ7, 258 W/Autojuicer, MC 2100, TFI, SummitRacing CDI, MORE SRS, Moser 1-pc, YJ tub on 1" body lift, YJ family cage.