The windows in a YJ hard top are glued in. They don't fit in a rubber channel. The piece that you see on the outside is merely a cosmetic piece to keep dirt out of the opening.
'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...