As I see it, the OP needs to fix the vacuum problem first. Without proper vacuum signals, the carburetion will not be tuneable. Any competent machine shop can mill the intake surfaces parallel with the current surface angle. loneagle had a good idea. Since you already know that the manifold needs milling, I'd cut some cereal box cardboard into gasket size and torque the manifold down, then remove the cardboard and check the impressions. Let your machinist use his best 'guestimate' to take off material. Recheck with fresh cardboard. When you get to an even imprint, top and bottom of the ports, you should be OK.
