The nut slot thing - After doing it from the string side a couple of times (without the correct nut files...) and getting it wrong here and there, I now take out the nut, and sand away material from the bottom. Too low? Add a shim. No nut files required, unless you make up a new nut. This of course assumes that your guitar's nut has the slots cut to the correct radius to start with.
And the fret level thing - I have found on several guitars (should not happen on real good expensive guitars?) that removing the strings, cleaning the fretboard, doing some fretwork, and re-stringing, re-setup and so on, will make some frets move in their slots, giving you high/low spots where you did not have before. So, all this is an iterative process, small improvements until you finally get there. I live in hope.