I too have been plagued by tooling marks or even self-imposed coarse sandpaper scratches that haven’t shown themselves up before a finish started being applied. I’ve often had to sand right back a couple of times before I’ve found and removed them all. Dampening the wood with metho, turps or white spirit can help show up these marks, but you still may not see them until you have at least some finish or sanded back the grain filler. If you do this, you need to let the wetting agent evaporate fully before applying any finish. Holding up the body to a bright light can help, and look at it from all angles, as I’ve found some marks only show up far when looking from a particular direction.

Glue marks on a non-veneer body are rare, but they can happen. But you can often get the same effect if you’ve sanded the wood with too fine a grit or pressed too hard in areas, so the surface becomes burnished and the wood doesn’t take up the stain in those areas very well. Note that the wood itself can sometimes just be awkward and have patches with awkward grain patterns that don’t take up stain as well as others. Scuffing the surface with a fairly coarse sandpaper and re-staining can sometimes help here.

Again, dampening the wood normally shows up these areas. You can use water, but it will raise a lot of grain and will require more sanding once it’s fully dry,

The front and back body surfaces need to be sanded ‘flat’ but the surface doesn’t want to be sanded too ‘smooth’ or stain won’t take well. You can have a very smooth surface that’s curved or undulating, but it’s not ‘flat’. For a good factory quality glossy finish, you don’t want to have dips in the surface. So sand it flat. A light mist coat of spray paint before you sand can help show the dips and pits remaining. You’ll sand all the paint off if you do the job properly. After that, I rarely sand above 180 grit on the body. Maybe 240 on a maple neck that’s just being lacquered. All the really fine sanding happens on the finish.