That is a very interesting manifold, Mike. I think that you are correct that it is a medium riser intake, but I've never seen one without the throttle linkage bosses cast in before. Just guessing here, but maybe the early '65 cars used some throttle linkage arrangement that bolted to the firewall or the carb studs, and didn't require a physical connection to the manifold. Perhaps later the throttle linkage was revised to bolt to the intake, and the bosses were added. Items like the throttle linkage bosses and vacuum fitting bosses can be added to the manifold pattern without a lot of trouble, so its not that unusual to see some variations in these, especially on the factory performance intakes.
It's also strange that the manifold doesn't have a casting number on it, but on the other hand I've got a Sidewinder without a casting number too.
If you wanted to measure the front and rear heights of the manifold, as shown in the drawing in the book, you could at least confirm that the carb pad height is the same as the 427MR intake I measured. That along with the casting date and the port sizes would be pretty conclusive evidence that it is a 427 MR intake.
From a performance standpoint the manifold ought to work the same as the 427 MR intake shown in my book, which is to say it is a good manifold. I'm glad to see you didn't port match the intake to the gaskets, because I doubt that the gaskets are a perfect match to the head ports. Your port matching job looks just about right to me.
Good luck with the project - Jay