I had this problem when I installed an 04 top and frame on my car. In addition to closing the latch when the top is in operation, you might be able to push the frame back.
This link https://sites.google.com/site/mikefocke2/installinga%2703-%2704glasstopandframeona%2797 describes the process for transplanting a top and frame. If you loosen the three bolts on either side that hold the frame in place, you can push the top back a little and this may solve the problem.
I know it worked for me, but the source of your problem and your results from trying this adjustment may be different.
Good luck.
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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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