I had the same issues with my '01 Box. My mechanic ran all the tests on it and said everything looked fine with AOS and was sure that the throttle body was causing the problem. He told me to clean it and sure enough, that solved the problem. All that carbon build up was causing the rough idle. This is a fairly easy repair, although taking off the intake box was a pain in the arse. Here's the link to the repair - Porsche Boxster Starter Replacement - 986 / 987 (1997-08) - Pelican Parts Technical Article
I know it says it's for the starter replacement but the very first part shows you how to remove the throttle body.
Hints**
You don't need to take off the hose that goes to the AOS to take the throttle body off.
You'll need a torx set to take the 4 long gold colored bolts that connect to the intake tube just behind the throttle body. (See picture in link below.)
http://www.pelicanparts.com/techarticles/Boxster_Tech/83-ELEC-Starter_Replacement/images_med/Pic2.jpg
You will need to disconnect some electrical plug on the bottom of the throttle body.
That's it!
Good luck!