Hi Joranaca, welcome to the forum.
setting the neck can be done after staining, as many find it easier to handle the neck and body as separate parts, then bring them together for the final finishing. It really is dependent on whether you have the room to work with the guitar in one piece, and whether doing it in one piece is really awkward or not.
For stains, I probably wouldn’t go much past 300 grit, as you run the risk of polishing the wood so that the stain doesn’t take to the wood. The consensus seems to have been 320grit maximum but some have had good success at 240.
It is generally recommended to do a wipe down on the raw body with mineral spirits or naphtha, this will highlight any shiny glue spots on the body that will need to be dealt with, before you can stain.
hope this helps, look forward to seeing your build take shape!







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