I have a 916cc motor in my 888, but it is done with a 916 crank and pistons in the original 888 cases. (Big end failure on original crank - no rev limiter you see!)
The 916 cases don't have bearings for the swingarm pivot while ST ones do.
I had to use 916 (ST4 actually) pistons as the 888 ones are the same bore but have a 1mm higher crown which would cause valve clearance problems. Valve sizes, cam spec etc is identical on 888 and 916 Bip.
This all used the original 888 wiring, injectors and P8 ECU, albeit with an FIM chip for an early 916 Strada and the whole bike is for sale if you want to copy it
If you have a read on the FIM website you probably don't want twin injectors unless you are going the full 955 SP/Corsa/120+ bhp spec.
Rob has put the ST4S motor in his 888 chassis and will probably be along with comments soon!