I looked into converting a ZX-9R to fuel injection a while back.
Pre 04 GSX-R750 throttle bodies have almost the right spacing, and I thought it was possible to modify them to work.
The 04 and newer are supposed to be narrower, but they went from (4) individual throttle bodies to (2) shared housings. I am not sure if they would work better or not, but they are definitely worth a look in my opinion.
I figured you could have used the modified GSX-R throttle bodies and either a ZX-12R harness/ECM/Power Commander or bought the aftermarket ECM from Muzzys as I do not think that the price differential would be all that great.