How flat is the neck?
Sounds like you need to run a long straight edge the whole length of your fret board to see where things dip. A long metal ruler or even a spirit level should do the trick as if you are that low at the nut your problem is most likely elsewhere and my bet is on too much forward bow in the neck.
EDIT: Just re-checked some of your build thread and as yours is a bolt on neck maybe you are experiencing similar thing that happened on my DIY Guitars closing down sale Tele where the neck sat too high off the body by about 7mm and caused me no end of intonation, pitch and action dramas.
Ended up using a block of timber cut to size and gradually sanded down where the neck heel joins into the body. Handy if you have a similar axe as a reference point otherwise you are flying blind. Towards the end I even used the metal neck plate as the sanding block seeing it was pretty close to the right size for area being sanded. From memory I think 120 & 180 grits were used otherwise it takes forever.
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