So if I understand correctly, you want to customize a few tables in your post but leave the default output for tables the same? Then what you’re looking for is shortcodes.
That should not be too hard. I think the hardest is Markdown tables allow for headings by having dashes on the next line. Supporting this feature means you can’t just parse the markdown and generate HTML at the same time; you would need to parse the second line before being able to display the first line.
Also, a nice HTML5 trick that may help you out testing things out before you change your CSS: the <style> tag can take a scoped="scoped" param so that it may be placed within the HTML body, and only applies to the style tag’s parent and siblings. This allows you to have both HTML and CSS right next to you when trying things out 