I've looked around the site and I cant seem to find any interface for private messenging.
What happens when I want to discuss a particular section of something with somebody specifically and I don't want to clutter up the comments section?
If you want to have a conversation of that type, the right way to go about it is probably to create a chat session and invite the other user to it. This should notify them in their "inbox" in the top left. Even if you are not online at the same time, your comments to each other will be saved (much like having a conversation through comments).
You will still be able to use it as an 'out-of-the-way' conversation, even though it is public if anyone wants to hunt around for it.