The square joint that you think comes apart, doesn't. It's a pressed fit.
The way that I replaced the boot on my previous YJ was to cut the old one off, then I put the new one in a toaster over for a few seconds to get it hot and pliable, sprayed it with some silicone spray around the ring, and forced it down over the square on the shifter. Once you get it warm, it expands easily over the shifter.
Hope this helps.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...