It could be done, for sure. It won't be easy, and you're going to need to fabricate things, but it's not impossible by any means. My 2 fav R1's have been my 00/01s and my 2012s. I love the rear traction and drive of the crossplane setup, and I absolutely love the fit and feel of my original R1s. If I could have the 2012 guts in an older frame, hell yeah I'd do it! I love everything about the ergonomics of those old R1s.
If you really want to do it, there's no reason why you can't. You're going to need the wiring loom, ECU, forks (for traction control if you're going for one of those models), fuel pump, airbox etc from the planker, but you should be able to fabricate up some mounts which will work. Having owned several of both of those models, there is enough room in the older R1 to fit all of the 09-14 guts. I've literally had both of mine side by side, and the older R1 is quite a bit bigger.
The one really big issue I see, is aligning the sprocket from the motor of the 09-14 with the rear sprocket. From memory, the 2012 motor is slightly narrower than the 2000, and you'd end up with the Planker motor off-centre in the 90-01 frame. You'd need to somehow extend the output shaft and sprocket to align properly. BUT... what would be WORSE is if the 09-14 motor is WIDER than the 98-00... you'd end up with the motor off centre in the frame. Or, you'd have to modify the rear wheel and chain channel, which depending how far it went could end up having to cut into the 98-01 frame. It'd be a big job, but, not impossible.