I didn't need to rewire my micro switches. I think Porsche changed the top transmission system for 2000 model year and my car had the same system as the 03/04 cars. If you started hearing the beep after you rewired the micro switch, I think you are correct that the beep is related. Check this link for some information:
https://sites.google.com/site/mikefocke2/installinga03-04glasstopandframeona97 I hope you fix the problem soon. The 03/04 top gives the car a more upscale feel and glass is simply better than plastic.