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.