Sounds like a very cool project!
There was never a late 50s custom color chart. Not that you COULDN'T get a custom color in the 50s, you could. But it was just
that... a true custom color. Fender had no standardized list of custom colors. The customer would tell them what color he/she wanted (or describe it), and they would go get it at the paint store. I believe it was around 1960 when they first offered a custom color chart with standardized finishes to choose from.
Therefore, all the websites are wrong (for example) when they say a '59 Jazzmaster in Shoreline Gold is impossible, due to Fender not having the color available. It was actually a '59 Pontiac finish
which would have been introduced in the fall of '58, and could well have been specified by the customer on a '59 Fender. San Marino Blue just happens to be a color that some customers ordered, it wasn't truly a Fender finish. In reality, any color you could possibly think of (that existed in 1958) would be appropriate to your Jazzmaster.
In case you haven't seen it, the best info on Fender custom colors is here (including the early 60s chart):
http://www.provide.net/~cfh/fenderc.html
Best of luck with your project! We're here to help in any way we can....
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