Two quick comments, six years after this was first published:

* I use this system daily and have shared it with probably hundreds of people in my org as a way to manage channel fatigue. It's a wonderful way to manage slack IMO. Thank you for writing it.
* The slack UI has changed a fair amount over the years, and the instructions on how to configure showing only unread could be updated (now in Preferences->Sidebar or context menu on each section.) Keyboard shortcut for Mark All Read is also outdated (it's now Shift-Esc).

Thanks a bunch for sharing this knowledge!