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I had them as /wp-conent/themes/themename/css/style.css

I ended up coding the full url paths (https://site.com/css/style.css) to the styles and js in the head.php file. Seems to have fixed all the issues. Oddly, changing the permalinks forced the current page’s identifier (e.g. “about-us”) to the front of all the linked resources. SOOOOO…. instead of looking for https://site.com/css/style.css, the page was looking for https://site.com/about-us/css/style.css. Interesting…

Tried it with an un-updated 2010 and the permalinks work fine. Site is quick, all the sub nav links appear. So, I can conclude that my theme is to blame. Problem is, I’m not sure where to start. What about changing the permalinks settings would mess with the js or CSS of the theme?

I know! That was a glimmer of hope when I saw the update…

Server cache has been flushed. No change.

The theme is adapted from 2010. I have done some light frontend work on it.

I ended up using a shopping cart… Massive undertaking, but an okay work around. WPeCommerce.