Hello, thanks for the reply.
I've fixed the user uploads problem, that was just simply due to a misconfigured .csv file.
The only issues I'm encountering now are 404 errors to do with enrolling in a course. (If a user clicks enrol, then are given the 404 page, if they click back and 'yes' again, the course loads fine).
When users try and upload a file that is too big they are given a 404 page also, this may be a normal response for moodle though, I am not sure.
IIS has all the permissions to the moodle directory, everything else seems to work with no issues except the things mentioned above.
It doesn't seem to mention a directory that is missing the address it goes to is: "http://moodle2/course/view.php", and just says this:
404 - File or directory not found.
The resource you are looking for might have been removed, had its name changed, or is temporarily unavailable.
enrol.php?id=24&confirm=1 is the link that users go to when they click yes to enrol in a course.