Dave,
There are 3 papers mentioned in the document but I don't know that any of them are where those numbers come from:
Effect of counterface roughness and it’s evolution on the wear and friction of PEEK and PEEK bonded carbon fiber composites on stainless steel, D.M. Eliot, J. Fisher, T.D. Clark, Wear 217 (1998) 288-296
Effect of carbon fiber reinforcement in the frictional behavior of PEEK in a water lubricated environment. J. Paulo Davim, N. Marques, A. Monteiro Baptista, Wear 251 (2001) 1100-1104
Effects of sliding velocity and applied load on the tribological mechanism of amorphous poly-ether-ether-ketone (PEEK), G. Zang, C. Zang, P. Nardin, W-Y. Li, H. Liao, C. Coddet, Tribology International 41(2008) 79-86.
To corroborate your 1.1 micron number I also have a [very short] presentation that was provided to me by Invibio regading their MOTIS bearing material on CoCr in a knee application: the initial roughness was 1.6 microns but after 5M cycles it had been burnished by the CoCr to 0.16 microns. I forget the specifics of "MOTIS" but I do know it's also a CFR PEEK material--just not quite the same as their normal filled grade (different fibers?).