Sorry I cannot help you in your quest as I do not know where or how the colors are stored for themes.
If you don't know already you should be aware of this issue. From the Knowledge base:
Externally created custom themes are not supported in FileMaker 12
Answer ID: 10880 Last Updated: Apr 19, 2012 12:34 PM PDT
Changes to the theme templates do not effect already created layouts. Only a new layout will use the new theme settings.
Are you (on OS X) pressing shift, ctrl, alt cmd when loading the theme? If not give it a go.
I tried this and nothing happened. What is it supposed to do?