This is solely my opinion so take it with a grain of salt:
Get over the "1 of 1" thing because it's useless crap - the value in this car is that it's a 4-speed 428 CJ ragtop and not anything more. You state production figures, which I can only assume you got from the Marti Report, but you fail to state whether this is a standard Cougar or an XR-7, which is a very important distinction to make (and therefore stating "1 of 4" doesn't tell the whole story. Marti is not 100% accurate, which is why it's a good idea to get a Emminger Report (sp?) to complement the Marti - records do have human errors at times!
I also believe AC cars could get 3.25 gears, but it may depend on the application.
What you should do is call Marti and ask him to explain the "Ford Research and Engineering" distinction because it may simply have gone to a Ford employee who worked in that channel. Have you seen Marti's explanation of certain things?
http://www.martiauto.com/faqfocus.cfm?qid=104
Sounds like a cool car (I'd love to hear more about it or maybe you can post the Marti?) but keep your excitement at bay and try to learn as much as possible instead of getting sucked into the puffery that sometimes exists in the hobby.