Moved installation to new folder, missing some things

So I moved my installation to one directory up from the original, I updated conf_global.php and most everything works except I seem to be missing everything that was in the uploads directory, however that directory was moved, and automatically updated in the storage settings. There is also no recache options like I keep seeing everywhere I've searched as the cache seems to be turned off for my site(for now). Any suggestions?

EDIT:

Nevermind, some of the things missing are from Applications/Core/Interface folder

EDIT 2:

Some of the links in the menu are still pointing to the old address, and some of them(forums specifically) are pointing to the correct address. None of my menu items have custom url, they all point to pages