1. I've created a course in Adapt authoring, however these course files don't seem to exist on my computer like it does after creating it in Adapt Framework, where are they held and can I edit the LESS/CSS on them?

The course files created by Adapt Authoring are in ;

{your install location}\adapt_authoring\temp\{your tenant ID}\adapt_framework\courses\{your tenant ID}

But that is only a build folder. If you make changes in the AT after editing in here they will override any changes you make in the folder. Builds from the AT are generated by the framework's core files. What CSS/LESS editing are you wanting to do? You can override these in Project Options for each course.

2. Is there a special way you need to use the Adapt authoring "upload plugin" area? Every time I download a ZIP plugin from the browser I seem to get a different error each time I try to upload it.

What plugins are you trying to upload? Not all from Github are compatible with the Authoring tool. You must look for the presence of properties.schema as a minimum. Also you can check out my compatability list at : https://docs.google.com/spreadsheets/d/1XDPyohslGe3bFrLo4U_Rr-muIzRVojnShYmmEKqOqnQ/edit?usp=sharing

Hope that helps.