I think I've pretty well concluded the architecture rethink discussed last week. After a lot of scratching around in the drivers and libraries that manage the SPI, I now have a version that works with all necessary elements needed to move to a single Arduino architecture.
It'll take a while to reconfigure the software to accommodate this change but I already have VFO frequency and S-meter displays working, so I don't see any particular issues apart from coding effort required.
At the moment I am using the rather ungainly hardware stack shown above. When the new display interface board is available in a few weeks time it will be possible to tidy this up considerably - the display will be mounted on the new PCB and connected to the display interface board via a standard 40 way "IDE" ribbon cable.
So, barring any unexpected setbacks I think I can safely say that I have, at last, settled on the best and hopefully final architecture for my Flex Controller.