*** SOLVED ***
Ok with the trial and error above and a lot of tips from the folks over at Yosemite ejects external drives I've managed to achieve stability.
Rig is Mac Mini 2011 / Thunderbolt Display / Westen Digital Thunderbolt Duo (daisy-chained to Display's additional TB port).
My steps to enlightenment have been as follows:
1. Perform SMC reset specific to your Mac.
2. Shutdown and disconnect Mac / Display from wall power.
3. Disconnect all peripheral connections except TB video cable.
4. Connect wall power. Boot Mac. Wait 10+ seconds before logging in.
*** Your system should now be free of display flicker issues caused by external HD instability ***
5. Shutdown cleanly and disconnect Mac / Display from wall power.
6. Disconnect video cable.
7. Connect TB drive cable to TB Display & Storage Unit. Attach Storage Unit power.
8. Connect wall power. Boot Mac. After chime, connect video cable.
9. Wait 10 seconds before logging in.
*** Your should now be able to see external HD attached (in my case) via Thunderbolt cable ***
10. Access System Preferences -> Energy Saver. Set both slider controls to ‘Never’.
11. Access System Preferences -> Spotlight -> Privacy. Deny access between Spotlight and External Storage.
12. Rescue External Storage content (if applicable).
13. Remove Western Digital Drive Management Software from Applications.
14. Format External Drive / creat new RAID set using OSX Disk Utility.
15. Shutdown cleanly. Boot Mac.
16. Access System Preferences -> Energy Saver. Reset defaults.
17. Access System Preferences -> Spotlight -> Privacy. Deny access between Spotlight and new external HD Label created in Step 14.
*** Stability returned to rig ***
Thank you to all for support and encouragement. I hope these steps help if you have a similar issue.