Dear Rob,
It's strange, probably something is wrong with how you upload the module. I suggest to revert back to your original changes using your backup. Then setup another localhost for my new module using my original procedure then import the new module *make sure they are all checked like in the attached screenshot).
Yes in my test here , you need someone to review the JS code because it's not compatible after I tested it in my module. It's a bit complicated. The easiest way to implement the Flex Slider module (how it is supposed to be used) is to use the default Slider post type then upload images for each post then you're done. Flex slider main images and thumbnail View will then loop to these posts images and display them as main images/thumbnails in sliders. This is entirely different in your case, you want images within a single post to be looped in a Flex Slider View. While I made some changes on the View, I see some JS errors that is beyond my control.
Please let me know if you are satisfied with my answer and if I can help you with any other questions you might have.
Cheers,
Emerson