I leave anything pinned or screwed down on the stock, excepting barrel, lock, and sideplate. So, patchbox, buttplate, inlays, thimbles, nosecap all stay on.
I leave the pins in the stock for the barrel so that they don't fill up with stock finish.
I put all the screws and small parts in a little plastic ramekin, which I then misplace, so I can spend hours looking for it when the stock is finished.