- Seriously consider redesigning the logical layout of the software. Some sort of rough MVC-ish pattern would be a huge improvement over the 'loop' in Wordpress which is almost impossible to deal with.
- I personally dislike PHP, but I do see its benefits in deployment.
- Make it easy to make beautiful typographic layouts. There's a reason this 1-page wasn't done in Wordpress itself; it is almost impossible to make 'hand-crafted-web' looks in Wordpress without deep CSS and HTML diving. Great blog post layouts shouldn't be that hard. Not all content is the same.
I haven't touched WP in a few years; does it have the equivalent of the Rails Asset Pipeline yet?
*This plugin hasn't been updated in over 2 years. It may no longer be maintained or supported and may have compatibility issues when used with more recent versions of WordPress.
As for the per-post CSS files it would be easy to do with a Posts custom field. You could take text input (CSS) and spit it out in the header using a basic query on the current post.