Craft, CSS Frameworks, Bower & Grunt setup suggestions
In my humble opinion, this is a task for Grunt / Gulp, not for Craft.

Addy Osmani has an excellent article on Environment-specific builds that would be interesting for you and the kind of use case you mention.

In short, gulp-replace or gulp-processhtml and gulp-preprocess will give you what you need to build such functionality in your build scripts. Similar plugins exist for Grunt as well.

As for file organisation, I generally keep my package.json and gulpfile.js files at the root of the repo / website. I find it a lot easier to manage paths.