Yeah, after having gone through everything closer, I realized that nothing actually needed to be added/changed. Just removing the the sections that refer to 'files' and 'blogs.dir' (I'm on a completely fresh install.
I ended up changing my config though and went with the fastcgi_cache method instead (in which the same above applies to this one as well) because I was running in to some strange behavior with w3tc.
At any rate, thanks for confirming the changes needed, and thanks for the tutorials, they helped a lot when getting things set up.
Another thing to note though is that I don't think the 'map $http_host $blogid' section is needed anymore either as that seems to have been directly related to the aforementioned 'files' and 'blogs.dir' sections. Can you confirm this?
Thanks again, and have a great day.