Having had air and water cooled dukes my vote goes to the 1000ie. I'm sure the S4R is a nutty bike, but waterworks add unneccesary bulk and complexity to a bike that was always designed to be uncluttered.
The other thing is I've never heard a bad word said about the 1000 monster. A storming motor with plenty of spec for later tuning. I currently looking for one for my 900 Superlight.
Good luck and enjoy whatever you end up. And make sure the list fcukers that torched your shed get a decent pasting....
Ali