I just had to replace the passenger side convertible top cable (broke while the top was up).
I did the same procedure of pulling the clips off the clamshell dampers so I could lift off the clamshell. then popped off the ball joints to open up the passenger transmission and replace the cable.
Mine went back on with no issues, (I just had to get the sides aligned) and then worked no problem.
All of this is to say: It makes me think you're right and something is off with the microswitch alignment.
This is a wiring diagram for a 2002 which shows how it all connects up that might be helpful.
http://www.richard-hamilton.co.uk/misc/porsche/2002BoxsterCabrioWD.pdf