yeah, when you think itbs the mind immediately goes to hella-cool venturi trumpets poking out of the engine bay. tough to do on a boxster, however. i was thinking of an approach like a 911 rsr:
http://forums.pelicanparts.com/uploads8/RSRTB1154376577.jpg
where the itbs sit between the intake manifold and head. this way you can still keep your maf and the ecu should work as before.
and there is the issue of throttle control. one option would be to use a flash for a cable throttle car and retrofit a cable system (ie, early 3.4 996 flash should work for 3.2 boxster with 987 maf housing; dunno what for larger 996 engines).
or you could somehow repurpose the tb electric motor to turn the throttle linkage. ive seen pics of the inside of a tb and it is just a gear on the end of the motor shaft turning a gear on the end of the throttle plate shaft. swap the throttle plate gear over to your new assembly and fab a bracket to hold the motor in place. put a motor on each bank and no need for linkages between the two. you would need to find a tps sender with the same output as oem, which i dont think is an issue.
this would be easiest if you use one long throttle plate shaft to operate all three butterflies (as per jakes); no linkages, and easily operated by a converted tb motor. my concern would be that, if we are reurposing the original, oblong manifold part as originally posited, then the butterflies would be installed along the long axis and max obstruction when fully open; put them in along the short axis and they wouldnt be as in the way when fully open. this makes the linkages a lot more complicated, however.