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65 Jazz Bass Question

Hi,
Just picked up a May 65 Jazz bass with an A width (1.5" at the nut) neck. One thing I've never seen before is that there seems to be between 1/16" and 1/8" space in the lower bout area neck pocket - in other words, the width of the base of the neck does not meet flush with the body's neck pocket. The finish in the pocket looks untouched. Has anyone seen this. also of concer, there is a randomly placed 5th hole on the butt of the neck separate and apart from the 4 screw holes to connect the neck to the body. The gloss finish seems consistent in terms of flowing into the holes and the 5th hole is smaller - possibly from a nail. Any thoughts? Pictures attached. Thanks!
 

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According to the vintage guitars website, which has a lot of Fender info, the nail dry method for bodies ended in 1965. I can't find whether there were nails involved in the neck glossing, but it might be there on the website somewhere. I like the article there about Fender painting methods and paints, very interesting. The neck must be stamped with May 1965- if that's the case keep in mind it can be months before they are installed on a bass body and sent out.
Update- Jim Shine's parts database under Fender neckstamps- you can see several examples of the screwside base of the neck- and they ALL have that 5 th hole!
 
RichEagle78 said:
One thing I've never seen before is that there seems to be between 1/16" and 1/8" space in the lower bout area neck pocket - in other words, the width of the base of the neck does not meet flush with the body's neck pocket.

The mis-match "ledge" becomes more apparent in the late 60's and 70's stuff, even really moreso on P Basses. You just about never see it on mid 60's stuff, but since the final shaping was eyeballed and done by hand it's certainly possible.