Howdy Graeme:
Yes, there are differences, but after '62 model year none of the changes were to help performance. In the 1963 model year the exhaust manifolds were changed to a donut type gasket rather than the flat gaskets previouly used. These are a much better seal at the head pipe. The diameter of the outlet was also increased to 2" along with the od of the header pipe. Some where around '69, earlier in Calif Exhaust manifolds were cast to accomodate a variety of smog and air injection requirements to meet EPA. None of these changes helped performance, by themselves, they probably disruptied flow. Exhaust manifolds were beefed up over the years also to reduce or eliminate cracking, a real problem on early manifolds.
I've looked at and measured the volume of the cast manifolds and while the internal volume varies, it is not enough to indicate that flow is improved. Some have reported a larger(?) 250 manifold used in Econolines. I have yet to come across any.
I prefer a pre-smog exhaust manifold from around '66 to '68. It is my opinion that the bungs and ports cast into later manifolds disrupt flow even though the later manifolds have a greater interior volume.
Stock manifolds can be improved on in several ways; mill the mating surface flat, enlarge the individual port windows to at least gasket size, blend and direct transitions, open the outlet to leave a minimal lip for the header pipe, finally, coat the exterior with Eastman's high temp paint to hold the head in- high temp=high velocity.
Before you start on any cast manifold check it thoroughly for cracks. Also know that the best cast manifold is no were as good as a good set of headers.
That's my two cents.
Adios, David