I finally got it !!!!. I'm so happy !!!.
It was the slash arguments. As described in Moodle: "Files (images, uploads etc) are provided via a script using 'slash arguments'. This method allows files to be more easily cached in web browsers, proxy servers etc. Unfortunately, some PHP servers don't allow this method, so if you have trouble viewing uploaded files or images (eg user pictures), disable this setting".
Initially I thought that I couldn't do anything about it because the Site Administration link wasn't working, so I couldn't access the Site Administration > Server> HTTP page.
Then I realized that this setting must be in the database. So I searched in the database for the term "slash" and I found the slashargument in mdl_config. It was set to 1 (on) and I set it to 0 (off).
All the links are working now.
I'm also not getting the "Input file not specified" anymore. I'm able to access the files.
Thank you so much to everybody that has input any idea.