My rig is stable and has been now for several weeks after months of torture.
I removed an 8Tb My Western Digital My Duo Thunderbolt from my setup and performed an SMC reset on Mac / Thunderbolt monitor.
I decided to re-arrange my workflow, replacing the WD Thunderbolt drive with a 5Tb LaCie to store legacy data only. The LaCie has a rocker switch on-board, although permanently connected to my Mac with firewire I only power it up when needed. Backups are performed by Carbon Copy Cloner on a scheduled weekly basis to a separate USB drive which I only connect for this purpose. I religiously eject each external connection manually and do not rely on a system power down.
My conclusion is that the newer drive interfaces have not been on the market long enough for all the bugs/issues to be ironed out with every platform. The 'Drive Not Ejected Properly' issues caused mayhem with my data and Thunderbolt monitor. The screen suffered bad flickering, a horror show for something costing so much. But this issue has also now disappeared without the WD Thunderbolt drive attached to it.
Apple/Intel have a lot to answer for here. They are clearly not admitting to these problems and instead seem content to push on with USB-C and Thunderbolt Mark 2. The lesson for me is to never embrace a new interface (Thunderbolt in my case) for my data so early in its lifecycle. Its very disappointing that so many users are having the same issues with the USB-3 on older Mac's. After all, we bought our machines in good faith.
It will be interesting to hear of anyone having these problems with a 2015 Mac shipped with El Capitan.