Hello.

Somebody has gotten something turned around. All 65 K codes came a 4-speed manual transmission, and the vast majority of those were the top loaders, which was indeed made by Ford. Some of the K codes didn't have the top loader, but, most did. The earlier 65 Shelby GT-350s came with an aluminum cased Borg/Warner T-10, for example, and, I have no problem believing that Ford would have put a cast iron cased T-10 in a K code if they had run out of top loaders on the assembly line, but, your car almost certainly came with a top loader. Many of the 65 K codes had the VIN stamped on the transmission, but, it would be on the top, in a place that you would have to pull the transmission to see it.
Agree !!!!! &...
Up through the 60's & early 70's, vehicles were not ordered as they are today. Yes, if you ordered package "X" it would come with 1, 2, 3.....but, you could also delete specific items within the package. As an example, our mustang (which has been in the family since it was new), when ordered as a GT, my parents really didn't like "trumpet tips" through the rear pan so the dual exhaust was a "delete" (as shown on the original order papers which we still have) and upon delivery, it was off to the muffler shop for a set of pipes.......a very common practice- which because of this it is not impossible, but I will say it is much more "challenging" to not so much verify something is a factory GT by having all of the items listed, but more difficult to verify it is not..and Ford was not the only one doing this either, a very common practice by the Big 3.
Dealers also dealt with quality control issues....and had a pre-approved budget by the mfg's to effect repairs....there are documented stories and pics where mustangs were delivered to the dealers with the trunk lids wrapped and sitting in the back seat....Customers could also pay an additional fee (typically $300) for the dealer to "special prep" the car prior to customer delivery...while each had a different name they called it...basically the dealer had the mech's go through the cars from nose to tail checking every single part, fit & finish...making it right. These cars typically looked, ran like fine tuned machines as a result...you could see, feel the difference.
My neighbor worked for GM in Long Beach, Ca back in the 70's, and clearly recalls special order deletes, hand carried orders to install "X" cylinder head on a particular car- he also recalls there was seldom more than a week went by that the cylinder heads didn't change (as far as port matching/sizing/shape)- as it was all dependent on the supplier and that varied by each shipment….or someone wanted their pickup painted the color that was offered on a particular car…..not a problem as long as it was built at the same plant (for an extra charge of course)- which also explains a few very, very ID pates.
While it is a wonderful thing to have a variety of people who have done such exhaustive research on these and other vehicles, we must also remember that the customer service and deliverables of the time were much, much different than today and paperwork, was, well, not the focus. This has lead to benefit us (especially in Calif) who became exempted from smog testing/cert because of the absence (disposal/non-retention) of documentation of our cars, but in all reality, even if all the paperwork did exist, it wouldn't do little to validate much more than is known today about the cars- because the paperwork was not a priority, delivering what the customer wanted was.
There were also 3 HiPo 289’s….the common 271 hp, 306 hp and only in the GT350R, producing 350 horsepower, weighed 75 fewer pounds, and featured an enlarged fuel tank (34 gallon vs. 18) for racing. With “special heads”, a super-duty suspension, racing tires and more, it was offered in 1965 only
just an FYI