Depends on year of guitar older fenders were shot with cellulose laquer as are most instruments test in the cavity where trem springs are or under pick guard. IMO cellulose laquers are best for instruments as they dont need the protection from sun & wheather as cars do they are still the finish of choice in quality instrument building you can mix any powder pearl with for colors or utc (univeral tintinting color) which can be picked up at any of your local paint stores not auto but plain old paint stores you cfan also use anhaline dye mix with laquer which is like a candy it can be used as a stain or as a shader depending on application & it is transparent you can actualy have a deep black that you can still see the figure of the wood hope that helps as I use to build Guitars which is how I got in to painting MoJoz
Find out what kind of paint is currently on it. Nitro cellulose is best for wooded instruments becuase it lets the wood breath and the wood resonates better and we all know that a good instrument resonates well.
The newer stuff is like what you would spray on cars so if you have the poly paint and clear on the guitar then I would do like you said. Scuff it, base it, flame it, clear it.