Darrin,
What Geoff is suggesting is that you a) forget about trying to space the gap at the spider, and b) instead focus upon the gap at the bottom of the clamshell where it meets the sill.
The gap at the bottom of the clamshell by the sill should be correct....and in so doing, that will set the gap and alignment at the spider edge for the lower windshield. Said another way, you place a spacing bump stop of some kind at the lower edge of the clamshell by the sill (to get the right gap there) and then adjust as necessary there to get the gap and alignment right at the spider edge above.
Of course, some folks use a seal around the edge of the spider to provide a little weather protection, but that seal isn't really for spacing/alignment.
I hope that helps!