Thank you for your response.
As a quick test I manually copied the SmartSearch Folder to ~/App_Data/CMSModules/SmartSearch/ which was missing.
I am now getting some results returned in my MVC app, so thank you.
I just need to diagnose why the folder is not being synced there in the first place.
The Task list is empty in the Web Farm modules tab. So I imagine my problem is around this area.
I did not use the Kentico.Search package, I did write my own based on the code from there however.