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Sometimes those 2 pins can be a problem. Especially if the car is not sitting level. As planojc mentioned, loosen all the nuts on the windshield so that you can move it as needed, then align the 2 pins, then tighten the windshield back up.
Before you tighten the windshield up, now is the time to snap the 5 upper snaps of the soft top to the car. It is easier to get your fingers in there before everything is tight.