Here is my problem, normally I convert asciidoc documents to HTML (or more precisely asciidoc --> docbook --> html) but here I've been given a markdown document.
I would like to be able to produce an HTML document from that markdown document that would look the same as if it was coming from an asciidoc OR be able to convert this markdown to asciidoc somehow?
Try to use Pandoc to convert the markdown source to docbook xml.
From there, it should be possible to convert the docbook xml to html with the same technique as you used before for the asciidoc input, e.g. use the same xslt-translations for docbook->html.