I can’t offer a solution for the ultimate workflow, but I can make some suggestions based on what I do. I also use Things, and I have an area for the company where I put all bugs and feature requests. When a user mentions an existing bug or feature request, I can increase the count to track the popularity of an item. For each release, I create a new project and add all the to-do items that I want to complete for that release. I usually schedule items based on when I think I can have them done by, which gives me a pretty strong indicator if I start slipping my schedule.

[As for everything else, I use email for all communication and don’t use Github, so everything stays in email or Things.]