Jimmy's advice as always, is dialed-in. I've got a shop, and access to nut slotting files, so I'd only be bypassing his strings affixed to wood blocks. That's a great hack though, and to tell the truth, I work with of a lot of wood nuts (on upright bass) that some homemade files would be better suited than the chainsaw and gunsmith files I have modified for use.
You had the right idea, but just had things a little bit backwards in determining how much clearance there is. (if I've read and understood your post correctly)
Instead of fretting at the first fret and measuring clearances at the second one, I put a large guitar capo on between the second and third frets, and measure the clearance from top of fret to bottom of string at the first fret. That's how you get the 'zero fret' effect Jimmy J's talking about. Getting there is another thing... if your nut is evenly high, then yeah, just flat file the bottom of it a few thousandths so all four strings come down the same amount. If you go too far, use the adjustment screws and raise it up. Make sure you keep it vertical when filing. It's easy to drift, so check your fit often.
Just bring it by tomorrow... I'll fix you up. It ain't but 3500 mi. Leave now and beat the morning drivetime rush. 😄