From your description of the problem and from exploring your site, it appears as though your path's are all messed up at some point in your code. Those "not found" messages are the result of the server trying to find files someplace other than where they are; the webserver will "read the other folders" in your directory if it is properly instructed to do so, but if you describe those directories incorrectly, then of course links to them will fail.
If you have used "localhost" in any of your paths, this is at least part of the problem.
Without knowing how your application is built, I don't know where to tell you to look for this - possibly in a configuration file?
IF you have such a file, post it here (with things like usernames and password obscured if they are in there), and someone here may be able to spot the problem.
Other than that, we would all just be guessing without seeing your code.