Though Mr. Alexander's admonition to leave the barrel in the stock is good advise, there are times when it simply is not possible. I try and leave the barrel in the stock as much as is practicable.
I am usually working on finishing simultaneously... While waiting for a stock to dry, blueing parts, for instance. And I always take the barrel out for finishing anyway, because I like to finish the insides of my stocks as well as the outside. It is my belief that this helps the water resistance of the stock. However, once finish is applied beneath inletted parts like a patch box or side plate, I immediately refit those parts, and wait for the exposed parts to get dry before removing them again to allow the covered parts to thoroughly dry. This helps prevent the wood from swelling to the point where the iinlay cannot be refitted.
Matt