If you read about alignment problems it is something that changes with time and won't stay correct over time, especially in a fiberglass boat. And the method to do it correctly seems to be a bit of a controversy.
I have no opinion on flushing the transmission, never did it. I've had three Yanmar boat diesels in two different boats, operating them since 1995, and never saw transmission seal leaks and no one ever suggested flushing it. I would suspect that while the fluid might help, you probably should check to see if you have something else going on. I never did anything but check the level on the dipstick. Not sure why you have engine oil in there, shouldn't it be transmission fluid per the book?
I would suggest you install the new motor mounts and do an alignment. The Yanmar owners manuals say that engine mounts need to be changed out after so many years as preventive maintenance- I forget the actual times but it was like 5 or ten years, anyway not very long but probably depends on the usage. The forty years that all these Morgans have is definitely outside the window.
We changed out our Yanmar 3QM for a Beta 38 because we couldn't figure out the shaft problem and didn't want to spend another summer disabled. Comparing the two I would say that the Yanmar 3QM is not a well balanced engine and had so much vibration that it probably was what did in the engine mounts, but maybe it was the other way around. Anyway if we had investigated better and learned of the broken mounts before they actually were pulling the engine, we might still be running it.
I hope you can figure out your issue or if you even have a problem.
Good luck,
Steve