3 Days Ago
Bob, what kind of glue are you using? Normally with woodworking glue, if you clean off the excess with water, then after everything dries, sand off the raised up grain and whatnot, there will be no stain when a finish is applied after. With an epoxy, pretty much the same, but although you can clean up with hot water (hot water also works better than cold water with white or yellow woodworking glue to remove excess), isopropyl alcohol or acetone works better to remove excess epoxy. There should be no stain to interfere with the finish if you remove excess well.
You can finish things first before glue up, but a finish shouldn't be where you will apply glue to join or it can minimize the strength. It seems to me that cleaning off glue over a finish or stain already applied is more likely to cause problems. Not really advisable. If you do want to go that route, after removing the excess glue and it dries, lightly sand after. You may need an additional finish application if the linseed oil or whatever turns whitish or the water or sanding has messed it up in some other way.
Fine steel wool made for woodworking (#0000) is good to use to blend and buff out a finish and remove irregularities. Good to use before a finish too, as it buffs up and smooths the wood very nicely. I usually use sandpaper to 380 or 4 something, then steel wool. Wool works magnifico on end grain.