Hi craynetworks !
1.Please open templateDetails.xml file in templatesja_pyrite folder, find following code section :
<param name="ja_color" type="list" default="default" label="Color Variation" description="Color variation to use">
<option value="default">Default</option>
<option value="red">Red</option>
<option value="green">Green</option>
<option value="orange">Orange</option>
</param>
this is code for define color .
2.Open templatesja_pyritecsscolors folder, this is folder what stores css file for color option,
3. Please open index.php file in templates/ja_pyrite folder , find following code section at about line 43 :
<link href="<?php echo $tmpTools->templateurl(); ?>/css/colors/<?php echo $tmpTools->getParam(JA_TOOL_COLOR); ?>.css" rel="stylesheet" type="text/css" />
this is code for switch css file for color option.
As you are requesting heavy customization, I am afraid that you have to handle the changes at your end.
i hope obove instruct can help you !