You have problems with distributor and throttle cable for two easy ones I can think of.
Everything exists on the early blocks and the later ones, just swap the heads over if they are still good.
Either mess with the engines, or screw with some wiring and the throttle cable. I guess leaving the engine together SOUNDS easier, but if the engines are both out of the vehicle, it's going to be easier to swap heads IMO, besides how "clean" it will be to leave the distributor wiring intact.
As a matter of fact, I'd probably pull the bottom end apart on the old one to make sure its still decent, use new bearings on the crank and rods if it needs them, and run IT until it dies. Of course makes sure the heads are still "flat" before swapping them. Just an idea.