That's probably a good question on one of the R1 forums... I only say that because I know a lot of folks running BMW, Honda and Suzuki but not too many R1's.
There are several aftermarket ECUs out there that would work well and might be easier to use than the hacking software.
We ran a power commander 3 (the latest when I built the 1000) that worked fairly well.
The records are actually lower in Special Construction, but that will require making some major changes.
I would probably run in MF, the best chance of adding what ever power you need with N20 as long as you keep it rich when on the button...