Throttle bodies on the 996 are a larger diameter. They are the same on top, but the 748 TBs taper to a smaller bore below the throttle plates. There may also be a height difference in the bell mouths, but I am not 100% sure on that one. If you actually use 996 Superbike TBs, they have duel injectors per cylinder. You can use single injector TBs out of an ST4, ST4s or 916 SBK. They have the same bore diameter. You'd need a single injector chip, which is a popular mod on the 996 anyway. If you decide to go with the duel injector TBs, you'd just need the correct regular 996 chip for your set up.
Other issues to address, not so much as the bump in displacement, but in model years. What year is the 748 you are working with? If it's an 98 or older bike, you are dealing with single phase charging system. You would only need to get a three phase regulator to go with the 996 engine. All 996 are three phase and this would be a simple plug and play. The harness doesn't care if the DC comes from a single or three phase generator. Plug is the same. If your 748 is 99 or newer, no change to the regulator is needed. At some point, maybe also 99 and up, the neutral switch changed causing a change to the harness as well. Easy fix, but it does need to be addressed. Two wire plug on the older bikes, single wire on the newer. You just need to modify the ground point.
Last thing I can think of is engine mount bolt diameter. Earlier bikes are 10MM and newer bikes are 12MM. This needs to be addressed according to what you're dealing with. For example, if you're trying to install a 1999 996 engine into a 2001 748 frame, the 996 will have 10MM bolt holes through the cases. You'd need to bore the case bolt holes to 12MM, or sleeve the frame holes on the 748 down to 10MM. If you have an older 748 and are using a 2001 996, then the engine will have 12MM holes and the frame 10MM holes. Most just drill the frame holes to 12MM, but if you don't want to mod the frame, you'd have to sleeve the engine down to 10MM.
The 748 (not including R and RS models) did not come with an oil cooler. Best to install one for the 996. You might luck out and get one included with the engine, but typically not. Lines cooler and fittings would be needed.
Airbox is the same, intake tubes are the same, exhaust is the same and the harnesses and ECU are the same. You'd need only the chip.
I'm interested in this mod as well. I have a 1/2001 748, donor engine is 2000 996. Frame bolts should be no problem 12mm on both. For the T/bodies, would you simply buy a used set of 996 dual-injector spec, and 996 intakes? Would you then run it with the second injectors disabled (unplug amp connector) and run the single injector chip (Ultimsp UM-222 or similar)?