Update: FIXED.
Others may not be so lucky with this but I was able to find a fix.
Luckily I have a dual boot on my Mac, so I rebooted into my old OSX 10.9. Using the old config I was able to access the MX860 configuration and updating settings. I then tried a PRAM reset (power down, press power on and immediately hold Option, Command (⌘), P, and R – don't let go of the keys until you hear the boot chime twice).
When I booted back into El Capitan all is now working fine with the MX860 (printer and scanner).
Note it is possible that the PRAM reset alone solved the problem, it may not have been necessary to boot back into the old OS but since it is now working I have no way to confirm that.
Hope this helps someone!
Scott