After a few weeks of use I can again report that my system has been solid as a rock, whilst using Pro Tools, however I was getting some weird random freezes in other apps. My instinct was telling me it was a graphics issue, but I did have a slight niggle that it might have been USB related.
I spent some time trying to get to the bottom of this with no joy, so I decided to 'bite the bullet' and try Clover, set was not as straightforward, but I followed the guide and after a bit of fiddling I got everything working (except imessage/facetime).
My system has now been running for about a week without a single lock-up or freeze in any application.
So I think it is very worth giving Clover a go, I did note that I was having problems with the detected iMac SMBIOS setting, but I used Clover Configurator and changed it to Mac Pro 3,1 and everything was fine.
I might add that at no point did I need to go into Windows to get the thunderbolt working. As soon as I selected 'Legacy' in the BIOS everything worked.