Re: 3 speed M/T to 5 speed M/T - Google is your Friend
There have been hundreds of articles on this conversion, both in print and on the Internet. The "trick" is to realize that, whether or not a Cougar owner wants to accept the fact, the Cougar is "just like a Mustang" (from the engine by to the rear seat footwells); and there are a lot more early Mustangs than Cougars out there being converted to a T5 (or TKO) manual transmission.
So, just go to Google and enter in "Mustang" and "T-5 conversion". There are at least 10 pages -at 50 results per page- on the topic. Some are basic how-to articles like the previously mentioned Mustang Monthly article, some are vendors offering kits from basic to all-inclusive, with clutch activation parts, crossmembers, and transmissions.
One thing to understand right off; the model T5 that comes closest to fitting an early Cougar will come from a 79-93 "Fox-body" Mustang. From that assortment, look for transmissions from the later-model cars; as a "factory-stock" T5 from a 1979 four-banger Mustang may or may not stand up to your 289, depending on driving habits.
You could even do an "Advanced Search" right in this Forum and find some threads on the subject. It's very common with today's prices.