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The paint goes on with minimal trouble, but the clear coat can be a real bear.
Just curious what problems you were having. Also what finish did you apply?
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Does anyone have experience or ideas on dying a white bone nut to match the rosewood fretboard, or the black tuning machines?
From what I've read, there have been varying results with dying bone, and there seems to be minimal absorption into the bone. A lot of people that have tried it, wound up buying a black nut (corian or graphtech) or nut blank. Alcohol based leather dye was a common product used.
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How do I set it in the right position, leading straight out?
Pages 9-13 in the PBG Manuel discuss temporary bridge installation, scale length and neck alignment. Fairly straight forward procedure. You can always ask questions on specific aspects if you get stuck.
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Next, what is the best way to fill the small spaces between neck and body?
Typically the gaps with a set neck are quite narrow because it requires a tight fit in order for glue to adhere to both surfaces adequately.
Therefore most gaps will be filled when the final clear coat is applied. This may require some extra thought if you have two different top coats on the body and neck (Tru Oil on neck, ???? on body). I think using the same clear on both body & neck is more common.
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Third, I have stained and TruOiled a little too much of the neck heel. How much do I have to do to rough it up so the glue will take?
You should sand the heel back to bare wood* at any areas where it will contact in the pocket. You can sand it back within a few mm short of where the edge of the pocket stops (ie: where the neck becomes visible out of the pocket).
*A little bit of stain left shouldn't be an issue, but definitely remove the Tru Oil.