Well you seem to already have solved your problem, but if you haven't it might be worthwhile to consider using Latex, the ToC and everything else is already han

Well you seem to already have solved your problem, but if you haven't it might be worthwhile to consider using Latex, the ToC and everything else is already handled or its very likely that a plugin already exists. You can also have separate files and just include them on a main file. Converting Latex to Markdown is also pretty seamless so it's (relatively) easy to convert to use in your website.