The reason I retracted the post about the client-side counter script is that responses from the Neocities API are missing a CORS header and that prevents browsers from loading the data. Reported it on github.
Regarding your theme copyright concern, you are safe. There are two aspects: its code and its graphical elements. Since you wrote the code yourself without even having access to the original theme ("cleanroom rewrite"), there are no potential issues. As of its look, a simple arrangement of geometric shapes (no matter how nice it looks) is not copyrightable in most places.
Cool site. One thing though: please note that a Creative Commons button is meaningless when it doesn't link to a specific license (BY, BY-SA, BY-NC-SA...). Any of them would conflict with "all rights reserved" in the footer, too.