When I open my convertible top, normally, the clamshell closes after the top is down, then the windows wind up. The top is fully open, but it seem that there might be a microswitch to tell the clamshell to now close, but it is not closing, and the window is not winding up.

When I close the convertible top, it closes fine, and the clamshell closes fine. What can I check to see why my clamshell is not closing with the top open?

I recently replaced my passenger side window regulator. Could this have anything to do with it? I was wondering if I reset my limit switches properly after replacing the regulator.

Car: 2009 997.2 Cabriolet.

 

I think you're in the right path. My best guess is that is either the micro-switch, a loose linkage or clamshell motor (check if it receives power). You need to remove the carpet below the space where the tops retracts to access the mechanism. Plenty of Youtube videos for that.
This top has a very special sequence of events mostly triggered by micro-switches, in order to be successfully completed during open and closing. I don't think that the door window regulator should affect that, as the auto up/down windows sequence (when operating the rooftop), occurs after clam-shell is fully open or fully close. The problem should be actuators/switch associated to the clamshell. Other area that could affect the clamshell not to close is the switches that tell roof is completed retracted or fully (securely) extended.
Regards,
FlatSixS