Answer to Question 1
Sunspots, which rotated across the Sun's face, showing that the Sun was not perfect and it (and Earth) could rotate on its axis.
Answer to Question 2
Pluto is so distant that its disk was not resolved well, and it had no discernable gravitational influence on Uranus and Neptune (Lowell's prediction was just luck). But Charon's orbit let us find the mass of both objects, and the series of eclipses allowed us to calculate the sizes of both bodies with great accuracy.