I'd suspect the distributer itself. When I worked for Ford this was quite a regular issue and happened to quite new cars. Being totally unexpected in nearly new vehicles, all sorts were checked and changed without any effect to the poor running but a distributer change solved it totally. Totally inexplicable as to why and how this happened but that became the cure for these cars with the symptoms you describe and was totally transforming. The CVH engine really is an excellent power unit and in a Morgan it can really show its worth, especially the injected XR3i version although I really did like the normally aspirated original version which was used later in the XR2 for quite some time.
