I measure height of first fret. Add .025" and tweak down from there. String tension (tight/floppy) will have a lot of bearing on final height. Tight = lower action, floppy = higher action. When you think you can make a couple of more light passes with the file, STOP. Make sure all strings are tuned to pitch during this process.
For rough cutting the slots I tape a peice of material to the fretboard at the nut that is 025" or so thicker than the height of the first fret and file down to it, then tweak as necessary. It's easier if the strings are not installed or or loosened and held out of the way.
Saves a bunch of string in and out of the slot/tuning to pitch to check the initial cut.