As far as side window seals are concerned on a YJ hard top, the rubber trim that is around the outside of the window has absolutely nothing to do with the window leaking.
The window is glued in, and the rubber trim is basically just what it is, trim. It is not any kind of a seal.
'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...