I presume this gap is on the fixed glass on the soft top, not the hardtop. Assuming the door glass is aligned properly to the windshield pillar when fully up, I would look at the fixed quarter glass adjustments. Sorry, forgot about the regulator change, I owned an 88. I seem to recall an elongated adjustment at the horizontal bottom of the quarter glass where the top pivots to lower. Also the metal piece bonded to the bottom of the door glass bolts to the regulator and I believe those holes are elongated allowing fore/aft movement.
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