The draft tube in the valley interferes with the intake.... Not the external tube but the one inside the block. I also recall having to plug the fuel pump rod hole if running an electric pump?
One good way to retain the 8BA ventilation is to cap off the front vertical stand pipe, install a pcv, and run the vacuum hose teed to both sides of the intake bottom. Use the 59A fuel pump stand and filter/oil fill to allow fresh air into the engine. The 8BA does have a small oil feed to the fuel pump push rod that should be plugged if an electric pump will be used, to prevent a small oil psi loss.
All years of intakes will interchange. The earlier blocks used more bolts, but this changes with the type and brand of non-stock intake used, ie two carb, three carb, etc.
Just so happens I just did the same thing. In my case the pop off valve for a blower covered the hold down bolt in the center, so I had to drill on each side of the intake passages of the 8ba block. You may not have to.
Flathead Jack has the plug for the pump if you go that way, also a chrome rear breather where you can fill the motor with oil. I did have at one time an early intake someone drilled for the draft tube up front, depending on the intake you have you might be able to do the same. On my blower intake I plan on just using the rear breather, no draft tube.
Any flathead intake will bolt up and run on any flathead block.That is not to say that there won't be any extra unused bolt holes or bolt holes in the mismatched intake that may have to be "falsely plugged" to maintain a complete appearance,but they should function alright.