@Ed Seith is the man for this question ! 
Synner Official Website
Oh boy. Not an easy thing. It does involve taking the rusty parts OFF the guitar completely.
You can ball up some aluminum foil, soak it in vinegar and rub the rust away, or you can get a can of naphtha (nasty stuff) and mix 3:1 with 3-in-1 oil, and soak the rusty parts in it to loosen the rust. Both solutions have been known to work.
Either way, you're removing the rusty parts entirely from the guitar first, and then taking those parts apart to soak and/or scrub them. A fun weekend for all!
You can ball up some aluminum foil, soak it in vinegar and rub the rust away, or you can get a can of naphtha (nasty stuff) and mix 3:1 with 3-in-1 oil, and soak the rusty parts in it to loosen the rust. Both solutions have been known to work.
Either way, you're removing the rusty parts entirely from the guitar first, and then taking those parts apart to soak and/or scrub them. A fun weekend for all!