I installed a "3 body lift on my '87 and now I'm trying to get some shifter boots to work. Any ideas? Thanks
Get rid of the body lift.

Seriously, 1" is the max I would lift the body. I bought a Samurai a few years back with a 3" body lift and it was the first thing I pulled off it. Installed some 3" RRO springs that a buddy gave to me and it rides/trails much better.