So, you're modding Guitar Hero II, and you want to...

General (file extraction, disc building, terminology, etc)

Scripting and configuration

For further reading, I'd highly suggest you take a listen to (and read the companion slides of) Eric Malafeew's talk at GDC 2005 on Harmonix's homebrew scripting language. The knowledge will serve you very well if you're doing a deep dive into custom scripting.

Chart-related

For further reading (especially while I get this section written up), check out the C3 authoring documentation. It's for Rock Band, not Guitar Hero, but the stuff about authoring guitar is still fairly applicable.

Audio-related