Greetings,
Mr. H. Nice. MY opinion is realign the engine/transmission with your shaft. From the looks of it, your transmission mounts will act as a fulcrum and the height of the front of the engine will determine the angle the flanges will line up at.
Front of engine too high=gap at bottom of flanges.
Conversely, front of engine too low=gap at top of flanges.
Flanges should be within .003" of parallel or better.