Did you already investigate whether the shaft mis-alignment is because the
engine mounts need to be adjusted or renewed? Have you checked the integrity of your engine's bed and bolts through the bed? (Has the boat been repowered?) How is the wear on the cutlass bearing?
A heads-up about flexible couplings, here is a quote out of Dave Gerr's "Boat Mechanical Systems Handbook": "It's ... vital that the shaft coupling match the
engine mounts. Soft mounts should have very flexible couplings, slightly flexible mounts should have slightly flexible couplings, and rigid mounts should have rigid couplings."
Also, for vibration reasons he recommends to not have more than one shaft diameter between the prop hub and bearing housing, however that's probably more a rule for power boats, and 1.5 to 2 diameters is probably ok for sailboats.