Hi,
I think what you need is pretty simple.
For the first thing. Each option would be associated with a class name On clicking an option, a script will be injected into the page which will change 'body' element's class name to the associated value.
For the second thing, having your custom css file. There is an option in the API to inject css into the page as well. So you could fist inject the css file, and then again the javascript that changes the body element's class name.
In short, I think I can do this for you. I've done a Chrome extension before and am fairly familiar with the APIs. Let me know if you'd like to talk further.
Just so you know, it's now not possible to load a private extension into Chrome from your computer - you will have to publish it to the Chrome Webstore to be able to use it without alerts. (but you can make it private there)