My individual runner SOHC intake is a Hilborn fuel injection setup converted to EFI. I drilled and tapped each runner for a 1/8" pipe fitting and then ran a steel line from each runner to a sealed box in the middle of the manifold; I get the vacuum signal from that. You could do the same thing. Your idea of running the hole through the flange of the upper manifold is an interesting one; I think it would work, but I don't know how a connection between the ports right at the manifold would affect the engine's operation. Running a tube from each runner to a remote box adds some isolation between the runners, and that may be important. But I'm guessing; I don't know for sure. If it was me I'd stay on the side of caution and use the tubes, because they will work for sure.
On the throttle butterflies, my SOHC has a 2.3" intake valve and a 2.43" throttle butterfly, and the throttle butterflies are too small for the horsepower level of my engine. On the Weber setup I tested for my book, the throttle butterflies are 48mm (not quite 2"), and the intake valves are 2.09" to 2.25", depending on the dyno mule. This manifold worked really well up to about 550 horsepower, but fell off after that. So I think your 52mm Pinto throttle bodies ought to be just fine if you are shooting for 600 horsepower or less.
Your project sounds really interesting, and I'm looking forward to seeing your intake manifold when it is built!
