The pots should be the ‘medium’ shaft length. The short shafts are for fitting direct to a scratchplate. The mediums should fit almost all holes drilled through wooden tops. Some older guitars may need the long shaft pots if they have very thick tops, but they are considerably longer and though I’ve bought some, I’ve never found a need for them. You can use nuts and washers, but they’ll sit very high in the control cavity and that looks weird.