What is the finish now? Is it clear? Color? Is the fretboard rosewood or maple? I'm not real sure on fenders but I would think they are laquer>? Usually at the factory on bare wood they will put down a clear sealing coat & sand it with a fine paper to smooth it over, apply the color coat then put a bunch of clear on top, finish sand & polish.
The neck depends on the fretboard. If it is rosewood you would tape off the top of the fretboard, on a maple freboard you paint the whole neck minus the frets. Fender uses a semigloss clear on the neck to give it a satin finish.
The hardware is all replaceable with aftermarket parts. Easily found online. A good source of parts & finishing supplies is....
www.stewmac.com