I bet this is one of the most common errors for new builders.
Unfortunately, correct nut position is EXTREMELY important. I would probably just ditch the bolt and go with a traditional style nut. Corian is a good material, you can get samples for free at Home Depot and it comes in just about any color. It cuts easily and can be polished to get it as shiny as desired. A brown to match the walnut would look nice or a simple ivory to mimic bone. It's my go to material for nuts.
I prefer traditional nuts as it's easier for me to dial in the action at the first fret. I use frets that are ~1.17mm tall (crown height) and I simply lay a nickel (1.95mm) up against the nut. I then slot until the file hits the nickel. The resulting action at the 1st fret is ~1mm.
What scale length did you use? I use the below website for laying out all my necks as it allows me to use whatever scale length I want and it produces a printable template.
This is the prewired pickup I was talking about....this isn't that exact same one that I used before but I am sure it will sound pretty good
Pickup string height: there isn't a set height for every guitar, every pickup and every person.
Best thing to do is what every professional setup tech does. Lower the pickup as low as you can get it before the adjustment screw comes out of the pickup base. Plug in the guitar and turn on your amp. Slowly adjust the pickup up towards the strings while you play til you get the right amount of volume output and the right tone.
Setting the pickup at the highest possible setting gets you more volume output, but not always the best tone.
You can set the high string side of the pickup higher than the bass string side for more treble or vise-versa for more bass. Even height for balanced tone.
Another good nugget: If your volume and tone are always set to 10, then the only way to get more is walk over to the amp and adjust. So set the guitar's volume and tone to 8 and then adjust the amp volume and tone settings to the best level. Then if you need more volume or extra bright tone, you have room to adjust for it on the guitar.
Scale length: scale length for regular guitar is 24" to 26".
The longer the scale length - the better the harmonics and higher treble pitch. 25.5" for the Fender Telecaster and Stratocaster gives rich harmonic levels. Those guitars have always been treble rich guitars tone-wise.
The Lower the scale length - the easier it is to bend strings and a lower tone. Gibson, PRS and Dobro live in the 24" to 25" scale for a more mellow tone and good string bending technique.
I personally like the 25" scale length because it's right in the middle, good harmonics, not too bright and still able to do good string bends without punishing your fingertips.
Hi, just another tip on pickup height. Getting too close to the strings with the pickup can allow the strings vibration to be effected by the pull of some magnets, creating a loss of sustain.