There are some good guides on Renntech, you will need to register to view them (free):
Boxster (986) - Mods - 986 (Boxster) DIY - Tutorials - RennTech.org Forums
http://www.renntech.org/forums/tutorials/article/109-porsche-boxster-avic-d3-installation-instructions/
I have the facelift Boxster too and replaced my headunit a few years ago. As mentioned already, you will have to remove the CDR23, amp and CD changer as these are fibreoptically linked. Good news is you will get a good price for them on ebay.
I fitted a Pioneer 940BT nav unit and an Alpine amplifier, rear speakers and also upgraded the dash speakers. The door subwoofers are pretty good with a decent amp so I kepT them:
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