I'm sorry but this is bordering on development work and not pure themes as such. What you are proposing is beyond a straight forward theme folder added to the theme directory within Moodle and set within the course or category.
The idea of creating pagelayouts means you could in effect have one theme which has different styles for each of the pages by manipulating the css id and class selectors.
But given that this is something new and not well documented, and perhaps an idea that is yet to be realised, the avenues open to you, as I see them, are:
1. Additional HTML (Site Administration > Appearance > Additional HTML)
2. Accessing the YUI JavaScript Library which Moodle has already (moodle/lib/yui...)
3. Enabling Legacy Files ( Somewhere in the Admin settings try Site Administration > Security > Site Policy) similar to Moodle 1.9 Server Files
Mary