You should be able to find the colors in the stylecolors.css file. When troubleshooting any web development, I use FireFox with the FireBug AddOn. FireBug allows you to select any element on a site and view/edit it's properties. When working with skins in mojoPortal, I make sure to set the following in my user.config:
<add key="CombineCSS" value="false" />
<add key="MinifyCSS" value="false" />
After adding those to your user.config, open and save the web.config file to force your application to re-read it and this will cause the user.config to re-read.
You may also want to consult the Creating Skins documentation.
A quick look at the skin you asked about showed me that the colors your want to change are #545454 and #414141.
HTH,
Joe D.