first off try and geta fuel ingected bike as thatll be better
Mmm, if you have the experience to fix them that is all good and well. For just the home builder, I would recommend a carby engine. They are SOOO simple. No need for an ECU or anything.
I wouldn't run a CB900 though universal joints, you will need CVs.
fuel injection is alot simpler than everyone makes it out to be. and alot more maintenance free especially when your talking 4 carbs