There is no difference at all. My untouched til I got it 66 'S' car and 66 wagon have the same casting numbers and port/outlet sizes.
On another note, if you are stuck using early-A manifolds, find yourself a 60's truck drivers manifold to run on the passenger side. There is no heat valve but it is the same casting....with an outlet that small the heat valve and shaft took 30% of the cross section of the outlet out of the equation. Massive difference in mileage (from 14mpg to 17mpg average) and power (15.0's to 14.80's) in my wagon from the swap. casting #2843953
