Inside the engine it's the cam that makes a counter rotating engine.
Of course other stuff outside is different.

Don Dando wrote:
As a first blush at an answer, it occurs to me that the original engines may
have been counter-rotating. Are the replacement? Did you move the old
starters to the new engines, etc ad infinitum... There are several question
related to the old engines Vs the new engines that you may want to
investigate. When cranked do they both turn the same way? Etc...

Don Dando