THanks @michiel I've managed to do this and all is working well, it took some time as the guide isn't that great, misses a few steps and lacks detail in some areas. For example:
It mentions moving htdocs, but what is the point when a new stack will overwrite it all?
No guide about how to move data between linux instances (sftp).
No mention of setting permissions on /moodledata/ or on any mod or theme folders you move across
Assumes that you are migrating to a new server with no moodle instance (I moved to the debian moodle appliance) which threw up a few errors (for example I had to drop the moodle database where the guide just says use mysql to update the db)
A few other issues I can't quite remember
This is just constructive criticism, the guide does give a general overview and after a good few hours I got there in the end.