I had the same problem when I swapped an 04 top and frame into my 2000. I'm assuming you are aware of the instructions on Mike Focke's web site: https://sites.google.com/site/mikefocke2/installinga%2703-%2704glasstopandframeona%2797
I was able to reduce the gap on mine by adjusting the top tension cables. (These are the cables with the ball and socket arrangement that you must pop out to put the top in service position.) There is an adjuster above it (a brass-colored nut that is about 9mm). Turning the nut clockwise (if I recall correctly you may need to experiment) reduces the tension on the back edge of the top and allows it to fold easier.
You need to be careful that you are not increasing the gap between the top and the clamshell when the top is in the closed position. This could lead to a leak.
I was never totally able to remove the gap without a little push on the clamshell. However, it seems to have become smaller on its own after repeated openings and closings.
Good luck and enjoy your glass window.
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2000 Arctic Silver/Black, Hard Top, On Board Computer
PNP Rear Speakers, HAES 6-Channel Amp, Avic Z140BH,
Painted Bumperettes, 2004 (OEM) Top, Homelink integrated in dash with Targa switch, 997 Shifter, Carrera Gauge Cluster with silver gauge faces, heated 997 adaptive sports seats, Litronics, silver console
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