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How much would it cost...

Yes, and -if possible- will cost an arm and a leg, possibly more. Consider getting a standard MIA Jazz and then replacing the body with an 'undrilled' one from Allparts, etc.

good luck!
 
^ I was gonna say that I don't think they make Custom Shop Fenders apart from the re-issues etc. and if you could get one, it'd be much cheaper to fill the holes with putty or something and refinish it. The other option is much smarter, but if you absolutely need to have the original genuine Fender body, that'd probably be the way to go.