dev site can't navigate to any secondary pages

I am not sure if this is theme related but any input would be helpful. My friend created a server for this and another site I am building for him with this theme. I am not sure if he did something in creating the stack or if it's something else, but when trying to navigate to /contact, /admin /user, anything beyond home you get a 404 error - more precisely: Not Found The requested URL /user was not found on this server. Apache/2.2.22 (Debian) Server at dev.videolube.com Port 80 Also I know, many links are wrong and need to be fixed, this was simple and I built it in a folder. - Not a good idea (I usually use subdomains), but it was simple enough to fix a few paths after migration. the broken site is at dev.videolube.com. That might become un-navigable as the DNS is being switched to an instance i created on my server which does seem to work fine. Also dev.videolube.com throws the following error: Warning: file_put_contents(temporary://fileSKQuG3): failed to open stream: "DrupalTemporaryStreamWrapper::stream_open" call failed in file_unmanaged_save_data() (line 1941 of /srv/lubedev/html/includes/file.inc). The file could not be created. There is a tmp folder. I noticed when he first moved the files some were missing like .htaccess but last night I replaced all the files with what is working fine on my server. Still broken. Any thoughts? I never saw this before. Thanks Matt