Nut disaster

So... I'm doing my first refret and I start to go to work on making the nut. It's a maple neck with maple fingerboard.

There was no nut in the neck when my teacher gave it to me. I don't know what nut was in it before, but the nut seat is wonky and not even square.
Not to mention, it's down through the fretboard on the bass side, and
almost through the fretboard on the treble side. I've taken
measurements on the inside of the nut slot, and I don't even know how to
go about making a nut for this thing. I don't think Warmoth would have
let a neck out of the factory like this, so my thought is that someone
(the owner or someone else) had previously installed a new nut. The nut slot just seems WAY too deep

The bottom of the slot on the treble side measures .0126", and the top of the nut slot measures 0.144"

The bass side measures 0.131 on the bottom of the slot, and 0.143 on the top.

A stock Strat type bone blank is a little too big for the bottom, but
there's a gap at the top when it's flush against the fingerboard.

Is there any way I can fill the bottom and back of the nut slot with something, and then file it square? The back side of the slot is filed at an angle going back just slightly.

Should I get a bigger, Gibson style bone blank and sand it down?

I can post pics if it helps... when my camera battery charges.

I just don't know what to do. Any help would be greatly appreciated!

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