Ford, at least in the 60's didn't make it a common practice to stamp VIN # on engines or transmissions. Actually to find one is quite rare--it is more common for GM to mark their engines.
Most Fords parts that do have VIN stampings are the truly special cars and engines, such as the Boss 302, 428CJ, or 289 Hipo K code engines--even then Ford didn't necessarily stamp them.
On your 64' Mustang, the best you can do is to verify that the engine installed has casted part #'s and dates that are near (and certainly not later than) the assembly date of the car. I believe that it is commonly accepted that most engine blocks, heads, intake, exhaust manifolds, etc. will probably have been cast maybe 2 months before the actual car build. It could even be as much as 4 months (or more) or closer to 1 month.
Because of this, and the fact that the Mustang was introduced at the end of 1964, most Mustang people will accept any 64' built 260 V8 as being the proper engine for your original 260 VIN'ed car.