@jjbaxter ,
You are using the wrong API call if you want to get a list of all of the courses. The API that you gave is scoped to the user, so you get a list of all of the courses that user is enrolled in, not all of the courses in the account.
The API call that you want to use is to List active courses in an account.
Depending on what information you need, you may also be able to use the GraphQL interface to the account with a coursesConnection. It allows you to specify what information you need and by limiting what information you ask for you can get more at a time (fewer pagination links). You can play around with the GraphQL by adding /graphiql to the end of your Canvas instance URL.