Thank you for your response! The website is http://www.withinepsilon.org/ and I use it as my teaching page.
Setting the link hover color doesn’t seem to appear in my Appearance=> Header. All I see is the setting for the header text color. It’s not a real problem because the CSS seems to work. I was just saying that it may make sense to have the header link hover color the same as the one set in the theme options as the default and have different colors be custom set by css. No problems though! 🙂
As for the fonts, I know how to change the site-title and the site-description font through the theme options. Id like to change the site-description (using the css id) font separately. (I like the title as a script and the description in sans-serif) Inserting custom css get’s overridden by the settings in theme options because whatever script that is generating the page is putting that css later than the custom css. One solution is to have the custom css be inserted after the css generated by the theme options, which I think is the default in the style.css.
I was just wondering if anyone has mucked in the source enough to know where to begin to make edits to the scripts that generate the css.