My thanks to Phil for his thoughful poste. My suspicion is that the fundamantal issue is laid bare in his second para:

Firstly we must understand that the output shaft on the S&S engine is designed to carry a sprocket for a belt or chain primary drive on a motorcycle. It is perfectly adequate for this application which uses sprockets and compensators of relatively light weight, causing little flywheel effect and all of the forces are within the length of the shaft with nothing overhanging. The application in the Morgan Three Wheeler fitted with the Centa coupling uses a relatively heavy outer rotor with increased flywheel effect and this rotor overhangs the shaft by almost double the length of the shaft. Add to this the fact that the wedging action of the rubber inserts in the coupling can produce powerful sideways forces and you will see that we have a much greater set of forces for the splined shaft to support than was originally intended.

First thought...."don't start here"....not helpful...

We have a live field experiment of a couple of thousand examples of the M3W running with very variable usage patterns and incomplete data capture - our (2012) version was initially built with v1 compensator, "upgraded" to Centa when the chassis was changed after a few years and has recently had the Bleazey mod done (when we found that the rubbers looked pretty well un-used). So our crankshaft is now enduring its 3rd variation in operation.

Phil's modifications to the Centa make huge engineering sense and we are very happy with what we have.

However, the whole engine/Centa unit in our cars is subject to a complex mix of vibrational forces that none of it was really designed to handle so the various changes are likely moving the points of maximum stress around in systems that have already been stressed in a previous set up. Likely consequence is that any failures are a product of this mixed history and a single root cause hard to identify. Phil's modifications mean there is now (by intent) a very rigid core to the system - does this concentrate stress somewhere?

Collecting field data to inform thinking is the only real way of finding our way through this.