How much are Neptune's and Uranus' orbits perturbed by Pluto and other KBOs?
Since (1) the mass of the Pluto/Charon system is very small compared with Neptune, and (2) their orbits are in 2:3 resonance, so the perturbation of Neptune's orbit would have been undetectable. University of Rochester has a good explanation of this. 


  The Accidental Discovery of Pluto
  
  Later supposed perturbations of the orbits of Uranus and Neptune suggested
  the presence of yet another planet beyond the orbit of Neptune.
  Eventually, in 1930, a new planet Pluto was discovered, but we now
  know that the calculations in this case were also in error because of
  an incorrect assumption about the mass of the new planet. It is now
  believed that the supposed deviations in the orbits of Neptune and
  Uranus were errors in measurement because the actual properties of
  Pluto would not have accounted for the supposed perturbations. Thus,
  the discovery of Pluto was a kind of accident