I actually had a very similar idea that I never really implemented but documented it in my notes a while back. Basically, it will revolve around "Deliverables"

I actually had a very similar idea that I never really implemented but documented it in my notes a while back. Basically, it will revolve around "Deliverables" or "Requirements" and everything will be tied to it whether an enhancement, a bug, issue etc. This way, all you need to do is roll up all your "deliverables" and you know where you are in the project in terms of timelines, issues,risks etc. JIRA is an awesome tool to manage issues/bugs (I use it extensively at work) but like you said, it is hard to keep track of a particular requirement/deliverable against the JIRAs. When I say keep track, I mean the ever changing requirements, customer priorities, new risks/issues that could hinder the progress, audit history etc.