I know this is nearly a one year old thread. I just ran across it and thought I would add some information.
The subject of leaf spring Cobra engine numbers is somewhat confusing especially the 260 engines and the last 60 some cars. The 289 cars, with exceptions noted later, have engine numbers stamped by Ford. They were production HIPO engines from what was being used in Fairlanes at the time. They are in an alphanumeric format and are stamped on a 'boss' on the left rear side (drivers side). Four digits with a prefix of PA and PB mostly, some other examples exist. The meaning of the prefix remains a mystery, at least to me. The four digits are a sequential serial number
There is also an assembly date stamped on a 'boss' on the left front side of the engine. It appears that groups of engines were assembled on the same date. Bob Mannel, author of "Mustang & Ford Small Block V8" has been tracking these dates.
Shelby purchased the HIPO 289 assembled from Ford. After SA added/changed a few things on the engine, it was installed in the car. SA would stamp the engine number in the space provided on the footbox tag. This is the tag that AC stamped the chassis number. Engines were not selected in order. The engine number does appear on the invoice from SA to the selling dealer or customer. While a number of cars have lost there original engine, many do retain their original engine.
The 289's mentioned above were '5 bolt' engines. Production ended on Fairlanes in the late spring of 1964 as Ford was gearing up for '65 production and the new '6 bolt 289. Shelby, by August of '64 was lacking engines. For whatever reason, it appears that approximently 30 '5 bolt' engines were assembled from parts at SA. These were stamped with a 'new' series of six digit numbers 000001 etc. (No prefix) So very late 289 cars in the higher CSX25xx area could have single digit engine numbers 00000x.
There were also 30 '6 bolt' engines used with automatic transmissions that used the same series of engine numbers.
I'll stop at this "muddy" point.[
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