The '79 manifold might have a few extra emissions ports and bungs. Should bolt right on though. The biggest difference is that your '66 manifold probably has a 1 3/4" outlet and exhaust pipe, while the '79 will have a 2" outlet, letting you put on a 2" exhaust system.
I saw the picture of your parts. The exhaust manifold may have a little bigger runner and internal volume, and bigger outlet, but I don't think the ports would be any larger. The Falcon Six handbook talks about the best years to use, and gasket matching to make the ports a little bigger. I'd find a bit older one to start with, as I see yours does have some emissions related bungery on it. Speaking of which, the aluminum carb spacer on the pile has an EGR valve on it or something. You might want to scrounge an older plain one.