What's the best way to link formal specs to JIRA enhancement requests?

I want to track changes to specifications using JIRA.

Ideally, I'd like to refer to a functional ID reference in a JIRA ticket (e.g. MYAPP>APPROVAL LOGIC>MAIN SCREEN), so that program managers can retrospectively categorise defects.

The reason for this, is so that QA scripts and documentation tickets can be searched/categorised meaningfully in the tracking system.

There seems to be a million possible ways to do this, e.g.

• should I write a custom component to select functional IDs from a tree?
• should I write the specs in confluence, or another CMS with a TrackBack facility?
• should I include a link to the documentation URL?
• should I use some other 3rd party plugin application?
• should I use some Atlassian application that i'm unaware of?
• am I using the wrong tracking tool/process to measure spec growth?

What's the best way, in your experience?