I had my S2R 1000 bored out to 1100 too and it was a great mod. I had all the work carried out by Moto Rapido but I'm afraid I don't know what the exact capacity or compression ratio was or, indeed, what pistons they used. I had a Power Commander III, got a custom map to suit the mods and it ran like a dream, (until I fitted lumpier cams and lost a load of mid-range torque for very little top-end gain - but that's another story!).
Although the 1000 and 1100DS motors have identical valve sizes, lift, duration and timing, the part numbers for the heads are different. (The 1100 Evo differs again with completely different valves and timing.)
I know that the design of the DS heads changed at some point, with the later models having a thinner journal at the left hand camshaft end and, because of this, they also have different end caps. (The aftermarket MVS caps I fitted came in two different inner step lengths to cater for both head types.)
It may be that the change happened when the 1000 became an 1100. (I believe that these thinner journals may have contributed to the oft-reported grinding noise on the Evo if the belts are too tight
http://www.ukmonster.co.uk/monster/s...ad.php?t=48249).
So, while some of the individual parts in the heads are interchangeable, (valves for example), the heads themselves are probably different, (but may well fit nevertheless).
Hope that helps.