i think it would be easier to deal with the 996 motor components for the sake of the alternator and timing pickups as compared to the older 916 styles. at least for the sake of the s4 ECU working correctly.

as for what parts are interchangable, i'd suggest downloading the spare parts sheets for both bikes and combing through the engine sheets EXTENSIVELY to size up what's the same and what's not.
996 biposto:
http://www.ducati.com/doc/cata...1.pdf

monster s4:
http://www.ducati.com/doc/catalogue/S4_Usa-02.pdf

cams/pullies are definatley intgerchangable between the two bikes, though you'll need longer belts to run the 996 heads. one issue to be aware of is limited clearance between the longer 996 horizontal head and the front tire on full suspension compression. also, not sure how much room there'll be for the battery and whatnot under the tank.
check out the "foggy owners" thread for some posts from infoage1. he's put some 916 heads on his s4 and may be able to help sort out fitment issues with you.