in my experience, when you replace any of the top gear transmissions you have to readjust the top to get it synched. there's a good article on pelican website, that's what i used for mine and it worked well.
check out the end of this guide, it explains how to do it:
https://www.pelicanparts.com/techarticles/Boxster_Tech/71-BODY-Convertible_Top_Repair/71-BODY-Convertible_Top_Repair.htm