In my experiences, simple pop-references and name-dropping are covered by fair-use.
Here is a link, you should find helpful:
The game design docs and guidelines should be a start for the basics.
I’d suggest you develop your story from an instinctual perspective - your background in lyrics should be enough to warn you when/if you have a question and running those by the community should provide feedback enough to get an idea. Eventually, you can even put a demo/beta up for feedback and testing.
To get an idea of how this works, you should visit the WiP sub-forum and sample a few active works, and there is the specific fora for code, off-topic and general game development.
You can also, once you have been a community poster for a bit, private message people if you have specific questions or concerns (including me) … most are very open, welcoming and helpful here.