Short answer- depends.
What year is your 1krr? You never really mentioned it in the initial post =)
Lambchops swapped a 1krr motor into an ancient 'Blade.... fuel injection and all.... also managed to switch the clocks in... but he is some kind of motorcycle genius (He will deny this to the end).
It comes down to your ability to figure out how to make something fit into a place when it was not truly designed to fit there in the first place..... It can be a bit of a nightmare to make sure everything lines up (engine mounting, ecu, wiring, sensors, coolant hoses, etc). The bright side is that, for the most part at least, while some positions of items may have changed the basics have stayed the same. I would think one of the biggest issues is making sure that the airbox fits underneath the fuel tank properly.....
Lambchop managed to go from carbs to FI, make everything fit, fashion a new loom, and .. I forgot what else because he did so bloody much to that bike =) Check out some of the later pages of his thread to find the 1krr engine swap into a carb'd '98 blade.
Link to said amazing thread that covers ALL the times his bike has been changed up My 900RR Winter Revamp
EDIT: you have it posted in the title what year it is... sigh... I'm sure I initially saw it too. I would check the fiche(s) to see the differences in cases, mounting points, and loom.