How you organize your projects tends to depend more on your needs but a logical structure is always needed and yours seems well considered.
Check out other postings on the same question:
I'll add that it can be hard to manage having a lot of script files at one level. Consider either putting multiple related functions into a script file (like a library), or create some subfolders to help organize.
Try to have a consistent naming convention. How you name things can be a topic of some religious fervor but pick a style and stick with it.
Definitely take the time to think about this planning and really have a setup in mind. It's not impossible to change things later but it can be a pain and if you can come up with something sensible up front, it's worth the time investment now.
