And have downloaded the extra content as well, but when I go into the installation folder there is no Extra Content! Where the hell does Galaxy put Extra content if not the installation folder?!

Will I have to download them again manauallly and wonder where a couple 100 megabytes of duplicated Extra content is sitting somewhere?

Select "Setting" in Galaxy and in the window that will pop up the last field says "Download extras to:". You should find your files there :)