I like I6's for the torque they put out however if you got the tornado replace it. I have heard as well from pepole that it sucks.
Engine swap shouldnt be to hard depending on the tranny you have if you have a 727 torqueflite (not sure if those came in 66) then the option are open to the Chrysler or AMC 360, 318, or my personal fav 440
If not you can just source the engine/tranny/Transfer case of your choice in there. Just have to fab some stuff.
Enjoy your FSJ i love mine wouldnt trade for a smaller jeep ever. Of course im fat so that maybe one reason