I have a 2003 Boxter S with a top that seems to be working just fine. However, there is a warning on the Msg. center which reads "top not in limit position." The indicator light for the top is on as well. The top seems to be closing fully and working as normal. Any ideas? Microswitch perhaps?

 

The warning is telling you that the top has not hit the closed limit. First thing to try is holding the close button for longer, to make sure that the drive is fully completing its cycle.
after that, check a workshop manual, I dont believe the switch is adjustable.