Taxi hi there,
In the earlier years when we used to use this type of motor mounting, which you are using now, the folded tin plate type - they were prone to cracking along the folded edge of the mounting. This was through, as you are discovering - vibration and slight mis-alignment caused by Dyco Couplings. These are not the best Couplings in the world, you get good ones and you get poor ones.
Ive included a picture of how I mount motors using 1/8 plywood, this solves the vibration problem in the motor. If you sit and think about the setup you have, with the motor mounting, you have a thin bit of plate holding the weight of the motor. As you have already discovered, you can quite easily flex the back of the motor up and down to alter the noise.
The other things is to think of, some of the thrust of the propeller will be transmitted through the shaft directly onto this vertical face of the motor mounting. This will depend on how much movement fore and aft you have on your propeller shaft and if it is any more than 1/16 of an inch movement fore and aft, you will see it will be bending the mounting of the motor.
Hope this is of some help to try and solve your problem.
Aye
John e
bluebird