Thanks guys. I knew there were double surfaces, but whenever I tried to delete them it deleted everything. Not sure what I was missing.

Now the next question: even when I tried to rebuild a surface using adjacent surfaces (like a blend, for example) it still would not join. why is that. What method did you use?

Also, even though it is now a joined surface, using the naked edges script still shows a ton of naked edges. How can it be a joined surface but have naked edges?