Same issue w/ my '65 273. I bought a later Edelbrock manifold and counter-sank the holes so flat head allen screws would sit OK (conical bottom) and slightly filed the bottom of the holes for screw clearance. I haven't run it yet to see if any leaks. Just a test fit, but seems to bolt tight enough. My main concern is sealing the water. The biggest problem is that on some holes the riser blocked my drill a bit. I initally tried an end mill in a hand drill, but it jumped around. With the countersink (or even a large twist bit), lean on the outer side of each hole.
Good info 340mopar on the self-aligning washers. I couldn't find them in McMaster-Carr and other places. Problem is $56 (if pairs) and not sure they can lean enough for the ~29 deg difference. Re oil leaks, in theory your crankcase should have a slight vacuum from the PCV. If a lot of ring blow-by, you will have leaks many places. I got some O-rings for the holes to help a bit.
I saw one aluminum manifold on ebay last year that claimed to be for 64-65, after I bought mine. I recall it sold for ~$150. You occasionally see the original iron 4-barrel manifolds, but there never were many cars with those.