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I'm putting together a les paul junior kit guitar, and I'm worried that the spot at the end of the fretboard (I don't even know what to call it, it's not a slot) where the nut will be is not totally flat, my prep sanding may have been overly enthusiastic. Any tips on ensuring that that space is true to the end of the fretboard?

I'm not sure I understand the problem, can you post a picture? Gibson nuts are thicker than Fender but not as thick as a Martin style (3/16 I believe). My plans show them sitting on the flat part of the neck (not the angled head). I make the entire top of the neck completely flat, then when I glue the f/b on I put a dummy nut in position, push the f/b against it and then knock it out after the clamps are on. Usually the head plate is on but I can also put the dummy nut back in place when I glue it on. Once you've glued the f/b on if the bottom of the channel isn't flat then true it with a small rasp, chisel, sandpaper.

I learned the hard way that the only way to get this "nut bed" (copy right applied for) flat is to use a small chisel. Anything else (especially sandpaper) will tend to round it off. Check the flatness by placing a small straight edge across it.

StewMac sells files which are perfect for this job... Pillar files.
I always called it a nut shelf... But that's not accurate for a Fender.

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"Act your age, not your shoe size" - Prince

Excellent, thanks guys. Nut shelf seems like a good descriptor, nut bed also works.

I think I caught my miss in time, I tried putting a dummy nut on and it wasn't sitting anywhere near flat which caused my worry, but noticed that some finish had built up where the fretboard joins the "nut shelf" causing problems, cleared that off and the nut sits nice and square now. I'll be much more aware of this from now on.