The color scheme gets changed in at least 2 places: StyleSheet and PageTemplate. PageTemplate is where the top gradient is defined. Just change the 'gradient vert #f81 #b40' in the top line.

StyleSheet is CSS that is put in at the end of the CSS generated by TiddlyWiki, overriding any earlier definitions. The majority of the StyleSheet is color, font or small position changes. One thing to note is the .header background. In broswers that render the top a a gradient per the PageTemplate, the .header background doesn't show. On browsers that do not render the gradient, the .header background color gets used.

StyleSheet is also where I've modified the layout to put the main menu above the content, rather than on the right, and change the location of the SiteTitle and SiteSubtitle to increase the difference between the text and the shadow text. See the #displayArea and #mainMenu sections.