If this was ten years ago you'd already have nicely used engine cases, but they are becoming rare.
Leaving out the 600 and 620.... 750 carb and ie, 800, 900, 1000 from SS and Monster 1000 and S2R, 1100 with mods, 1100 EVO with mods, S4R (996) with frame mods and S4RS (999) with frame mods. The engine bolt holes are more or less universal (smaller diameter on bikes a little bit later than yours)
You'll be able to use your excisting ECU++ on everything up to, and including 1000 engines. The 1100 too. S4R/S are not equal (enough) I believe.
Wiring issues?
Not all of this is plug and play. The closer you stick to what you have, the easier it will be. Like with the exhaust for example. Help is not THAT available as it was ten years ago, but we'll try