The 6cyl in the '66 isn't the original anyway, so, swap away! If the '64 is just a parts car, it should have all the conversion parts you need to put the 318 in the '66. Going to a 340 will require a bit more thought and conversion parts. Upgrades to the brakes and rear axle are definitely recommended.
Absolutly...if i go that route later on i would want an 8 3/4 in. differential also. Glad you mentioned the center link...don't think i would have thought of that !