My current plan for my first build is to paint the back and sides of my body black, and I have a quilted maple veneer for the top that I will be bursting green middle to black edge. I plan on blending the edge into the rest of the gloss black body. I am wondering what order of glueing the veneer, staining it, and painting the body should be. I think there are multiple possibilities that could work, but I'm wondering what everyone's experiences and ideas are about the best/most efficient way to do it is. Also, when should I drill the holes for the neck bolts and pickup mounting rings?

Thanks in advance,
id drill the holes first, otherwise you risk damaging your finish.
not sure what you mean by stain, paint and gle the veneer. are you staining it or painting it?

glue the veneer, then put your green down, then do the black, then do your clear coats. put toothpicks in the small holes (such as pickup mounting ring screw holes) so they dont fill completely with paint and such.

also, go see painting and refinishing thread for better advice and pointers.
I wasn't sure if I should paint my body before applying the veneer, or if the process of application would damage the paint/ finish on the other side. I'm thinking I might paint the body before applying the veneer then I don't have to mask it off when I spray the back and sides black. Toothpicks are a good Idea, I didn't think of that. Also, if I use some 3M tape on the cavities and neck ferrule area, will it easily come out after clearing without damaging the finish around it?
I've only ever seen builders do staining after gluing veneers to bodies.

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be careful with veneers as the glue can seep through a thin veneer and leave the wood impenetrable to the stain/dye. wood glue doesnt accept much of anything.
first thing to ask -
does the body have sharp or rounded edges? sharp makes it a definite line where the top meets the sides, rounded means you really WILL have to blend them together.
the problem with rounded, is that if the back and sides are gloss paint, and the top is dye/stain, black paint and black stain are completely different looking. theres not really a way to blend them together. if its a sharp edge, then it will be easier to paint, then tape it off, then dye the top, and just leave the corner as the divider line.
my solution was faux binding to separate them, but it didnt come out very well