Thank you so much for this mate - this is exactly what I was after! I have feeler gauges so no need to break out the paper. I'll take those clearances at the 1st fret with the strings depressed at the 3rd. The bone nut that I have has pre-cut slots so I guess I can use the current depth as a guide as to how much of the string protrudes above the slots.
Since you have feeler gauges (and if you have a decent set of verniers*) another tip/trick for roughing in the nut slots is:

*NOTE: if you don't have verniers, you can measure the fret height with your feeler gauge this way -
Lay a straightedge across the first two frets and stack the leaves until they barely slide under the straightedge. That's your fret height. (this is done without any string on btw)

> measure the height of your first fret (from fretboard to crown)

> add .030" to that figure

> stack the feeler gauge leaves (blades) to whatever that total is

> lay the stacked leaves across the fretboard right up against the nut

> file the slot until the file just kisses the feeler gauge - stop

> move on to your next string/file size (rinse & repeat)

Now you can put the strings up on the nut and go back and fine tune each with the string depressed at the 3rd fret as laid out before.