Thank you for the reply.
I installed MediaWiki by downloading the .tar.gz from the download page here. It's ImageMagick that is getting to me as it's a bit more complicated to compile and such.
I uninstalled ImageMagick via "sudo apt-get remove ImageMagick" and manually compiled it within /var/www/html/w/extensions/ImageMagick.
I am still having the "Not found" issue as well as thumbnails being broken. That'd be ImageMagick 6.8.9, the latest version.
I am guessing that it is user error because when I remove $wgUploadDirectory & $wgUploadPath from LocalSettings.php, uploading files works almost entirely fine.
If I change $wgUploadDirectory & $wgUploadPath, this is what causes it to break. I suppose my issue is somewhat resolved, but I'd like to figure out why it was failing.
I was trying $wgUploadDirectory = "$IP/images/public";. Path was the same. Then I tried "$wgScriptPath/images/public", but both produced this error on top of "Error deleting file" or "Error creating directory". Permissions never changed though.
Anyway, I'm going to make a new ticket because now the issue is different. "Error deleting file: Could not create directory "mwstore://local-backend/local-deleted/t/l/p"