Is it leaking on the top of the frame or at the bottom per chance? Or are you sure it is leaking through where the glass seals with the frame?
If it is leaking through the glass seal, those rubber seals that you see aren't doing a thing besides making it look better. There is some urethane seal in there on the frame flange that the glass is sitting on. You might need a touch up job on that.
Based on my knowledge there are only 3 places the thing can leak, on the top frame rail (not sure the exact set up on a hard top - never had one), through the urethane seal somewhere, or through the cowl seal (the most likely culprit).
1995 YJ Sahara