The original airbox fouls the 999 tank pretty badly, so I am looking at intake options. A pod filter setup would hopefully save some space under the tank.
I would still prefer to keep some form of airbox if I can make it work. At the moment I have not found a way of doing that with the 999 tank. Even with the open airbox cover or an MWR filter, I do not think I am going to get anywhere close to retaining the factory airbox in any sensible way.
I also do not think there is enough room to modify the underside of the 999 tank, and I would rather avoid sacrificing the tank to find out unless I absolutely have to. I think the rear of the airbox would end up very close to the top side of the tank, or at least very close to the filler cap area. I have not made any measurements yet, so that may still prove less severe than it looks. Even if I did go down that route, I am not convinced it would leave much more room for the ECU and battery.
I may soon have access to a 3D scanner, so I have also started thinking about designing a completely new airbox, and possibly making it in carbon fibre.
I have also been considering a setup similar to a bike by UNICO MOTO, with pod filters positioned just in front of the fuel tank. One complication is that I had planned to fit a steering damper in that area. I already have an Öhlins damper on the shelf, so I would try to position the filters slightly lower.
There are still a few details to work out, including what to do with the crankcase breather, possibly just using a typical breather filter and venting it to atmosphere. I am also not certain what I would do with the hose from the airbox to the stepper motor.
The area under the tank does not actually look too bad for room once the airbox is removed, so I am going to do my best to package as much as I can under there and keep the rear of the bike clean. For the exhaust, I am thinking about using some Termignoni silencers from an 848 / 1098 / 1198 (96116107B).