A while back I bought a Delta Grooves neck because, new to guitar building, I wanted to see how nice a neck could be. I finally put this into a nice Tabak box. Humbucker pickups, enclosed tuners, hardtail bridge.

The intonation is so whacked I gotta move the bridge back further. The sustain on this neck is beautiful. The humbucker is warm and gnarly with gain applied. As soon as I get the intonation fixed, I'll put a sound bite up!

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I think I might try filing the slots some more...

just had a re think Richard, another, and more likely culprit might be the nut being too high, that fits your problem well as well, as all played from the nut will be a little bit higher pitch, whereas if the nut edge is further towards the tuners, they will be lower pitch to get open tuning, but sharpen when fretted

Yup. I thought so from your first photo.

Your distance from nut to first seems too long.

You can fix this and there's a mathematical way to do it. I think.. And because it's 5 am here (I can't sleep tonight) better get a second opinion here from one of the guys..

Measure the distance from the first fret to the 13th fret (in mm). Double it. (This will also give you the correct distance away from the first fret to your bridge). Take that number and divide it by 0.9438743127. This should give you the position of the nut. 

You can check it out by putting a small nail at this measurement, not much higher than the size of your frets. This will act like a movable zero fret. See how it effects intonation BEFORE you make any changes to the guitar.

It looks like the distance from nut to 1st fret is correct: 1.431.

I removed the nut and sanded down the bottom edge some and now it's very close to proper intonation. I'll do a little more sanding...

Just a thought, but if everything is good except the nut location, could you move it to make things right?  A shim at the end of fretboard would move it back, or a bit of filing on the end of the fretboard would move it forward.  Hopefully the former as it is much less permanent! 

That nuts too high and the slots are contacting in the middle of the nut not the leading edge.
I learned this trick in luthior school.
First take a carpenters pencil and cut it length wise sand it flat on the side you just cut off make sure it's dead flat( sandpaper glued to glass plat works great for this and the sanding of the bottom of the nut).
You now have a tool to set the minimum height for the nut.
To use this tool. First unstring the git place pencil flat on necks fretboard on fret's 1,2,3 scribe line on nut with pencil tool this will give you a " do not go lower than this line".
Now take that measurement from bottom to line and transfer it from top to bottom of the nut. Now you can sand the bottom of the nut with out repeating putting it back on guitar and off till its close. Now that the nut is at the correct height you can address that nut slot you want the take off position to be as close to the fretboard side as possible. You will need to do some fine tuning but this will get you in the ballpark very fast and on your next guitar you will be able to quickly find nut height before shaping the top of the nut and not have this problem.
If it was me I would make a whole new nut out of bone as that nut looks too thin to cover that saw mark and I'm not sure what it's made out of but bone will always sound better than plastic. I hope you get this sorted out as that a nice start you got going on. Oh and welcome to your new addition.
Hey Shawn, I've seen that pencil trick but nobody's ever said how they saw the pencil in half! lol
I might jus have to sand it down using the sandpaper glued to a flat surface?
I just cut it with a box knife they split right apart.

The box knife did a good job!

I marked the nut, removed it, measured distance from bottom of nut to the line, transposed the measurement, and started sanding the bottom edge. Once I got fairly close, I slipped the nut into place. Intonation is almost correct. The screws on the hardtail are still screwed in as far as possible (springs are totally compressed) though....

Screws on hardtail fully compressed. Sure would be nice if I could back those screws off a bit!

Nut's a little lower now....

Ohhhhh... I didn't know I could remove the springs!

I had to do that with the last one of those bridges I used. I had to stick a plastic piece under the height screws on the low string. It buzzed once I got it pulled way back. Those screws are behind their little troughs, and at a steep angle. I used one of those little plastic things that attach tags to clothes.

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