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