Hi Paul, 

I just did something similar with the Resources extension. To keep things simple to start, I think all you need to do is:

1. Download and a extract a copy of the boxMenu zip file from Github.
2. Rename the folder, for example adapt-pauls-menu
3. In the bower.json file, change the name to your new folder and update other fields like version, homepage, issues, displayName, menu, and any other fields you want.
4. Zip up the directory again.
5. In the Plugin Management page, upload the zip. 
6. In your course, select the new menu (note: you need to do this every time you upload a plug-in to trigger a full rebuild or your changes won't appear)
7. Preview to test it out.
8. Every time you make a change, you also need to increment the version number in bower.json before you zip it up or the tool will complain you've already uploaded that version.

Development can be a little bit quicker if you're using the framework directly, but it's manageable to do all of your testing in the Authoring tool. (just a lot of zipping, and uploading, and triggering re-builds to remember). There are plenty of other files you'll want to update if you ever want to make your menu available for others, for example, the README file. But you'll stumble across all of those as you play around with the files. 

For my plug-in, I also did a bulk find-replace on all instances of the term "resource", "resources", "Resource", etc throughout the course and renamed everything to match my plugin name and stripped out the "contrib" part in any filenames, but I don't think that's actually necessary.   

Note: if you only want to change the colors/fonts of the menu, that's better done by creating your own custom theme based on the Vanilla one (steps basically the same as above).  Pretty much all of the basic CSS type stuff should be stored in there.  But if you want to change the behaviour of the menu, that's where you'd want create your own version of the menu.

Hope that helps,

Ryan