Join Date: Dec 2006
Location: The lovely Van Nuys, California, USA
First off, the 996 frame won't accept the large airbox without modifications to the box or frame.
The computer should be an easy fix, I'm in agreement with you about the eprom change. All of the injector control including DUAL injectors, is done by the eprom and switching it out with the 748R eprom will work since they are the same computers. The 996 supplies fuel to both injectors at the same time identically fired, so only using 1/2 of it should be OK. You will need a PC3 and full dyno tune to properly get it running properly!
The airbox is the biggest difference in the equation. The stock 996 airbox evidently has too little volume and the 748R airbox as just the right amount at 14L. The reason why they went with showers was not just for efficiency in air/fuel mixture (which its quite good at) but also for putting the TB's inside the airbox, so the airbox could get larger. Basically from what I've read, the showers were a necessity rather then a performance upgrade. On a 996, the large airbox and showers should give a small HP increase of between 4-6hp. Ducati didn't use the large airbox on any production bikes until the 748R with the Kyalami frame.
So, there you have it. If you can fit that there box in the frame, you should be in good shape!
OHH and PM me if you end up not using the airbox... I'd love to get my hands on one!