A true prototype is the original, handmade example from which the production tooling is based. A pre-production model is built after the tooling is created, but before the model is officially put into production. Most "Prototype" Jazzmasters on the market were built after most of the body tooling was done, making them pre-productions and not true prototypes. You can estimate the age of a pre-production based on what parts are true tooled Jazzmaster and what is hand shaped or borrowed from something else.
From what I can gather, there were at least three phases of prototypes. There was the offset-body design phase. This guitar had a Strat tremolo and jackcup. It also featured a 7 pole pickup Leo was experimenting with. Likely testing the string between two poles idea he later used on Precision and Jazz Basses. Fender still owns this guitar and is in their private archive. The second phase was the pickup, rhythm circuit, tailpiece and bridge design. Freddy Taveres had this prototype. It featured a Stratocaster neck. It appears that Leo had the tooling all set up after this phase and is why we see employee guitars using these parts with odd necks. The third phase was the neck design. This is when Leo first used rosewood for the fretboard and designed the Jazzmaster headstock. The late Scott Chinery owned what was likely this prototype. The neck was originally a one piece maple neck with skunk stripe that was machined for a slab fretboard. My guess is the roots of the Jazzmaster go back to perhaps as early 1956 with body assembly designed and tooled up by mid 1957. The final phase (the neck) was not likely completed until 1958.
so Leo likely was not in a hurry to get the design wrapped up allowing some time to let the world get used to the Stratocaster before unleashing the Jazzmaster.
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In 1962 Fender released the Fender Jaguar. The Jaguar's basic platform was the Jazzmaster <http://www.fenderjazzmaster.com>. Leo changed the scale length, some of the body design. The pickups were designed narrow and with a metal “saw tooth” like claw that was made with the intention of concentrating the magnetic field, providing a punchier sound than the Jazzmaster.
Metal control plates were added for visual appeal, but the Jaguar displayed Leo’s changing ideas about serviceability and ease of manufacturing. Previous models had all of the components installed to the rear of a pickguard and most of the solder work is done before going into the body. The Jaguar demanded it be wired into the guitar as each control section was surrounded with wood, only having a drilled hole for the wire to pass through.
The Jaguar had a flip mute mechanism, no doubt inspired by the mutes being offered on Mosrite and Gretsch guitars.
Pickups:
The pickups follow Stratocaster pickups in materials, but are different in a couple obvious ways. The magnets protrude from the bottom, and the wire eyelets are in the side rather than on a lip extension. There is a sawblade like frame around each pickup. This was made with the intention to concentrate the magnetic field for a punchy tone, not for shielding as the Urban Legend suggests. Originally the two shorter teeth are meant to go under the two plain strings (wound G strings were the norm in 1962), but they left the factory all over the place.
Tailpiece
The tremolo tailpieces only went through one significant change. The very first units are notable for their "Pat Pending" stamp below Fender. During the late 1961 -very early 1962 timeframe we see the switch to a patent number 2,972,923. This is a very important number as the number never changed on real Fender guitars. This number is almost always wrong on Asian forgeries made back in the 60's and 70's. I have seen real Fender's end up with the fake plates over the years!