...If memory serves, I believe that I heard .05 at the 1st fret but I cannot remember of that is true...and I have just spent 20 minutes or so trying to find a definitive answer. So...opinions?..
It's been my experience that using an arbitrary measurement is going to be an exercise in misery, unless every single instrument that you are going to modify has the exact same starting point, for nut slot depth and action at the 1st and 2nd frets.
As per what Baz said most of it I agree with, however I have some comments...
1. ONCE you already adjust the saddle for string action at the 12th fret, which CAN be arbitrary or absolute as per your classroom ukes, If you check the intonation of the first 1-5 frets with a tuner and find that the intonation is acceptable, i.e., not too sharp (or not noticable to the students or yourself), then I'd leave it alone.
2. If you sand down the bottom of the nut, you will lower ALL the strings by an equal amount, but since the strings are different diameters, and each have a different vibrating and parabolic arc, the thicker strings require more clearance over the first 2-3 frets to avoid buzzing, so I personally avoid sanding the BOTTOM of the nut and...
3. using needle files, a hacksaw blade or those torch-tip cleaners, lower the nut slot for EACH string individually FROM the top, until the intonation on that string is no longer sharp, the danger being you can go too low and now you have buzzing at the first frets, so you need a stop gauge of some kind...you need to GO SLOW and in SMALL INCREMENTS, with 100 classroom ukes this is going to take a few weeks maybe...I do not envy the task, and if I were local to you, I'd volunteer to come over and help you out provided you would supply the coffee and occasional pizza
4. StewMac has such a gauge that is like a set of [sorry corrected
NOT needle files but
FEELER GAUGES coffee has not kicked in yet] and a capo clamp combined (see:
http://www.stewmac.com/Luthier_Tool...Saddles/Safe_Slot_Nut_Guard_Complete_Set.html ) which I have replicated and use myself with a hefty rubber band to hold the stacked feeler gauges in place at the nut since I cannot afford to spend $85 for that tool and I do not make a living doing instrument setups
5. if you still take the nut slots down too far, you will either need to get a new pre-slotted nut or nut blank and start over, or you can fill the old too-deep-now nut slots with superglue and baking soda (see here:
http://www.stewmac.com/How-To/Onlin...Repair/Fix_a_broken_nut_with_baking_soda.html ) and start over, also see
https://www.youtube.com/watch?v=kn1z2R-w3i4 and
http://www.lutherie.net/nuts.html, and there was another video I saw recently that specifically showed how to fill the nut slots on an ukulele and using the superglue and with a superglue 'accelerator' made the process less painful but I cannot find it in my bookmarks or history at the moment...
Also, here are some videos from a longtime UU member John (OldePhart) [who has not been on UU for a while] where he shows an extensive setup on a Makala Dolphin uke, and attention paid to the nut slot setup:
Part 1:
https://www.youtube.com/watch?v=BXUcm_IAmTs
Part 2:
https://www.youtube.com/watch?v=MpuNNY1GUVY
I hate doing nut slots, and bone nuts take forever to cut down and round out, as well as the bone dust being toxic to inhale and at the very least you need to wear a painters mask (paper fiber held with an elastic) to avoid getting the dust into your lungs. If you inhale bone dust, it's nasty and the problem can take days to clear, dont ask me how I know, it's really bad once it gets in your lungs and throat,
just wear a mask.
Cutting nut slots is more iterative and painstaking than lowering or compensating the saddle because even 0.125mm of material removed may be either too much or too little to correct intonation, and too little, it's rinse and repeat, and too much and it's do-over time, so you have to go
really carefully, but you can do this with the strings still on and a tuner at the headstock. 2-3 strokes with a sharp file may be all you need to move the needle on the tuner, but a dull hacksaw blade on bone might take 20 strokes to achieve the same end result (I have no budget for tools)...
Nothing I said here is carved in stone and I'm sure that with the right tools it's a simple task, and professionals can do these things without much fuss, but these are what I've come across under my own hands...
(When I win the lottery, one of the first things I am going to buy is about $2,000 worth of tools from StewMac instead of hacking around with poor-mans implements, either adapted from other things laying around, or hacked up, all mainly due to having no tool budget, but these home-made adaptions I have technically 'work' but I feel that are inferior to the professional-grade tools that are purposely-built by StewMac. Maybe I will start a new career as a traveling guitar and uke setup helper...once I have the pro tools)
Hope this helps...