This is how I set up my guitars for a low action:

Set up the truss rod so that the neck has a very gentle curve in it - not much relief at all. Turning the trussrod nut clockwise (viewed from the hex key end) will straighten the neck, turning the trussrod nut anticlockwise will allow more concave bow in the neck.

As your nut height is high, I'd then recommend putting a capo on the first fret (or taping the strings down hard), so the effect of the nut is taken out of the equation. If you've got a chromatic tuner, then tune the strings a semitone higher than for open strings so the tension is correct.

Then look at the action from the 12th fret and above. I then adjust the saddle height so I can just fret and bend all the strings cleanly. I normally start with the saddles low and work up the action height until I can bend the lower strings without choking, and the upper (wound) strings which I don't bend far enough to be an issue, sounding cleanly.

Then look at the action at the lower frets. Using the capo has taken the nut slot height out of the equation so you get a good idea of what's really happening. Do all the notes sound freely without buzzing? The action at the 6th/7th frets may still feel feel quite high. If so, tighten the truss rod slightly, maybe 1/16 to 1/8 of a turn. The neck will be flatter and the 6th/7th fret action will be lower (also at the upper frets but it's the lower frets we're interested in at the moment). Do those low notes fret and bend cleanly? If so, you could try another very small tightening of the truss rod. Repeat until you start to get buzzing or choking on the low frets and then back off the truss rod slightly until this stops.

Go back to the high frets and test them for choking and buzz. Straightening the neck will have pulled the strings nearer the frets, so you'll probably have to raise the saddles slightly by a small amount. Once those upper frets play OK, then that's the time to take the capo off and file the fret slots. If you file them when the action is high and then lower it, you'll probably end up with 1st fret string buzz, so it's important to only do it once the rest of the action is sorted.