You know the trick with the flat pencil?

Sand a pencil flat on one side until the lead is flat with the bottom. Lay the pencil on the fretboard and draw a line on the nut. Add a little for the height of the strings itself and a tiny bit to compensate for wear and you know how deep you can cut your slots. I found this method helpful with my telecaster build. Have seen this on youtube and found it actually pretty smart.