I didn't have a gray box that were were speaking off under the text on my individual pages (about, leaks, music, events, goods). And since you mentioned it, I always remembered there being more information to edit on these indiviudal pages in the admin.
Instead, I unchecked the "Leave A Reply" stuff by going to the "discussion" tab under the settings on my admin page. Still no dice.
Funny thing is - the category link (or pages link) that appears above the picture in each of my topic posts, links exactly the way that I need it to link. For example, if you look at the most recent topic "The Siege has Sold Out in Japan" and you click the "Leaks" link directly above it, it will take you to the main leaks page. Now, all I need is for "leaks" link in the "main navigation menu" to target this link.
I know for sure this is not a css issue. It seems like it's more of a permalinks issue, but all my permalinks seem to be the same as they were when my website was working.