You'd be much better served (time, cost and yen-wise) by just buying a 4V K100RS:
Because of the way registration works here, it is cheaper to register the older bike, and the testing isn't so stringent.
1100's fetch top dollar, but K100's are very cheap.
Call it a mind experiment, I think the upgrade path would go something like this.
I believe that all tuning should start with suspension and brakes so.
1. 1100 Rear wheel (because it slots straight in)
2. 1100 front wheel, discs, forks, triple trees (yolks), calipers, fender (mud guard)
Then it gets tricky,
3. 1100 throttle bodies and injectors only? or 1100 complete engine with throttle bodies and injectors.
Any other parts that you wold consider as upgrades?