I spoke directly with PC in the US today regarding this, as I have an interest in your question, and they gave the following answers :-
The 916 does not have a dedicated power commander model, and PC dont really recommend using another one, from a diff bike unless its fitted by an authorised centre. They told me that fast by ferraci have had some success of retro fitting say 748 or 996 PC's to the 916, starting with a base map, then running the bike on one of their dynos, and making the necessary adjustments.
All PC's come with a base map, for stock bike, stock exhaust. So what you would be up against is different fuelling for the two different sized engines, Ie 748 or 996, so best to start with a zero map and build from there.
I reckon John Hacket maybe a good place to start for dyno and PC on a 916
ANY PC3 willl work,as stated you will need a custom map doing on a dyno though.I think mine was a 748,junked the map and re-mapped for the 888SP5,no problem.