Greatly appreciate the response Ken,
Your suggestions are all something I will have to consider,
In relation to the purpose, it's been decided that because out moodle instance is becoming so large that we will split them up by department (just trying it out in this instance but we have separate instances for external students and distance learners so why not) but since people have been progressively working on content with students they want all of their old courses (including data) taken across.
So far I have taken all the backups using the automated backup functionality (including user data) and written a script which uses Moosh to loop through courses and add into the relevant instance.
This does work but some courses were failing to restore due to the aforementioned issue with mapping role permissions, I'm noticing more and more that it appears to only happen with any course which didn't have any enrolled users, I have managed to successfully run through courses which do contain user information and these have restored sucessfully.
It may be that any course which fails I will have to manually restore as I am then presented with options to just bypass mapping the roles.
Thanks again for the response, I will work through your response (especially interested in breaking away from MNet so will spend some time looking into this)