As you found out, the crank register is the biggest problem. If you are going to get a different converter, anyway, just have it built with the early small pilot nub, and the late large internal splines. I have all my converters built that way.Most places don't charge extra to do that. If you just want a "stock" type converter, I am told Daaco converters has them available with the small pilot, and large splines. You will also need an early flexplate. These are getting hard to find.
Next you need to swap the oil pan and pickup tube between engines, but do not throw out the 66 pan and pickup tube. They are necessary to put a later engine in a early "A", and people are looking for them. Also need to use the later engine mounts and brackets on the early engine.
Any slant six head will swap on to any slant six engine, so you can do whatever you want in that regard. I would just keep the 66 head with that engine, as there is a greater selection of spark plugs available for the "drool tube" head, then the later head.
If staying with the 1 bbl carb, you will need to use the late carb, as the throttle linkage hookup is different. Maybe the choke, also, but I am not sure, on that.
Keep the crankshaft damper, and timing cover and tab matched, as the timing mark location is different between the two engines. They can be swapped as a pair, but don't mix them.
Everything else is just a straight swap
I think that is everything