Knee pain might also be that you are using too much muscle in too high a gear ratio for too long a period. And maybe at too low a cadence. Shift to a smaller ratio and spin faster.

It might have been mentioned, but a quick reasonably accurate way to set your saddle height is to put your heel on the pedal spindle and stretch your leg out straight. This eliminates the error you might get from simply putting your foot on the pedal and having it tilted without you realizing it.

It gets me within about a cm or less of the correct saddle height for me.