Glad to hear David! Looking forward to seeing it!
If the pegs are holding tuning, I wouldn’t even worry about the shellac being a factor. If you need to clean the shellac out, roll up a piece of 320 grit sandpaper and turn it around in the hole a few times.
The pegs should sit wherever they need to to hold the strings in tune. You’ll want to guide the strings downward on the peg as you turn to keep a good downward tension of the strings at the nut. This will prevent nut buzz.
The exception is the fifth (thumb)string peg. You’ll want to guide that string to whichever height you prefer- usually to the same height that the other strings are floating above the fingerboard at the fifth fret position if this makes sense- it’s uniform string height.
I never used a 5th string small screw (pip) on this type of neck. Because the peg passes through the fingerboard I have always used the peg itself as the pip. It’s a simplified way of terminating the fifth string and it in my opinion is better than a pip because it allows you to adjust the fifth string height (action) to suit your needs. I do use a small screw in necks that have the peg going into the side of the neck as you can see on other models on the site.