I stopped trying to figure out all the Easter eggs a long time ago.
I was obsessed with it in high school, though. I even tried to play the Creed Quest, but failed miserably. (I ended up making My own version of the Creed Mythos... it was so wicked. I wish I didn't lose so much of My stuff...)
I think a lot of it is just a mixture between happenstance and the clever placement of things to make the fans go "WHAT'S THAT MEAN?!" Kind of like Tool and bands like that, putting obscure references and weird imagery in their work.