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Paul I can assure you that the factory wheels where well used, however as I am a small rider, this may have helped save brake wear on the rims.
In the end I did sourced some hand built wheels with IRD aluminium rims, PMP hubs and Sapim C-X ray spokes.
If you look at top end factory built wheels such as Zipp or Enve, essentially they are still handbuilt wheels, so I ended up going down that route.
These new wheels certainly feel smoother.