You could exchange the exhausts and find out if it is really the catalyzers.
I don't think there is much difference (if any) in the programming of the EPROM, so you'd have a reasonable comparison.
FWIW, I don't think it's the catalyzers. Haven't heard anyone about a difference in engine characteristics.
And there is another thing: The V11 engine always gets smoother (and more powerful?) with more kms...
Easiest solution: don't ride it between 1500 and 3000 revs! The engine likes 4000 to 6000 much better imo.
Maybe someone else could give their ?