See the pictures below from the car dated before the restoration started - it looks like a regular GT Fastback but had numerous strange factory welds, a bigger rear window, strange vent cutouts and more. 

Let's have a look at the details: 
This car show unusal VIN stampings out of place of typical positions, although the VIN itself indicates a Fastback build on 19th. December 1964 in San Jose, 2 month after the first serialized productions were made. Actually on this day also some B/FX racers were produced acc. to the Haskell/Smart Mustang Production guide. 
Mike however at this moment follows the reports of that factory insider that indeed a few were made much earlier, which is quite natural for a factory to simulate production processes and some may have slipped or intended for being used as show or press cars.

The rear vents differ from the original and look like somebody tried something out in this area.

The rear window is 1/2" larger than the usual 1965 Fastback glass The interior shows some different trim caps. The original colour - analyzed with a scan - appeared to be similar to a 1963 Competition Orange (in fact a Chrysler colour)  Mike owns the car more than 25 years and when he registered it, he learned from the DMV that actually this car was never registered before. It showed only 2800miles on the odometer, when he got it. Let us know what you know about any other early showcar or custom or mystery fastbacks to give Mike some support and relief in his research.The car has been already restored meanwhile, but Mike could not stop thinking about the mystery alterations, he found during the resto. It is supposed to be not a serialized Shelby, but may have been used for a testfit of components acc. to that San Jose factory worker.

Dave Alzayer - who collects VIN information already for a long time, browsed for us his huge archive and came up with these other early Mystery Fastbacks. 

"Well, I found information in 1990/1991 Mustang Monthly readers sections about 5R09A144005, who claims to have  a more ore less "handmodeled Fastback rooftop" on a prototype that was "pulled off the assembly line". Acc. to the readers letter Ward and Karen Landis from Santa Monica bought this car in the early 80ies and that it originally came from a Fernando Valley Ford dealer - ordered in mid 1964 prior to the release of the 65 models. The response says, that it is rather unlikely that such a prototype woudl come from the San Jose assembly line, just speculating that a PR promotion vehicle could have been pulled, but evidence would be needed.

The other one is 5R09C131657 from then Dave Spangler from Houston with door tag codes 63A M 25 26H 74 6 6  that has a bunch of weird parts on it and questioned to the editors as an early Fastback. Dave says his was made August 24th., 1964. Dave sees evidence in the poor factory assembly work (such as missing trim attachment holes).
The editors recommende to contact "In Search of Mustangs" from Jim Haskell and Jim Smart.

Editors Note:
Actually the first registered Fastback there was 5R09C130711 built on the 22nd August for a long time....... well until October 8th. 2009, Mustang Monthly reports about 5R09K125001, the first San Jose car built on August 2nd, 1964, when they started building Mustangs. The first San Jose Fastback, the first K-code from there is a true survivor being used back then as a drag car.
 Check out their blog here

The first registered from Dearborn is 5F09K250009 - built 1st of August 64 and the first from Metuchen is 5T09T133029 dated Februar 65 (since Metuchen was later added for production of the Mustang).

So, if you have a VIN of a 1964 built early Fastback prior to those dates at Dearborn or Metuchen, let us know.