Nut Height Surgeons, Please
 

I just need a little hand-holding. I do NOT want to replace this nut.

I measured my fret height at .048". I am stacking two feeler gauges (total thickness of .051) against the nut and CAREFULLY filing. About 20 iterations so far. I am trying to get the .005" feeler to make contact between the 1st fret and the string, with the string fretted at the third fret. Once I am there, I may not have the guts to continue down to .003" or .0025".

In the meantime, I just want some hand-holding. Am I doing the right thing? Will I safely not screw this up, as long as there is .005" clearance at the 1st fret, with the string fretted at the 3rd fret?

I think you're spot on. I'd aim for the .005 with procedure you described: gap between the string and 1st fret while fretting the 3rd. This gives you some wiggle-room to smooth the slot with emery cloth or steel wool if required. As you may have guessed, it's really easy to overcut a nut...a few swipes of the file goes a long way.

Riis

Three thousandths on the short leg of that triangle is going to leave less than three thousandths at the first fret. Someone using a moderate attack will be able to cause buzzing in the lower register. You may want to stack a little bit more on there. Start with fret height plus .010". Once there, work your way down a few strokes at time. Remember to leave enough to polish the slot with 400 and 600 grit papers wrapped around a smaller file.

Surgery was successful. The patient is resting comfortably.

After filing the slots down to the feeler gauges (which were .003" taller than the frets), I still needed to file the slots more to get the 1st fret gap to .005".

I also learned that once you are at .005", or .004" or especially at .003", you have to be VERY careful.