Very nice write-up, seriously. It is clear that you lived through these pains many times over. I cannot agree more on how important the communication aspect is. Sloppy communication makes collaboration highly ineffective and the project often diverges from the desired path faster than you can sense it.

On the tools, I can also recommend an IRC-like element. A persistent searchable chat-room that can be used for real-time and deferred communications. HipChat (by Atlassian, the makers of BitBucket, Confluence, JIRA, etc), Slack, Ryver, Gitter (for GitHub fans), and the plain old IRC come to mind.