So, I had built a virtual host with ISPConfig - my path (linux) was /var/www/clients/client1/web1/web/. There was also a link in the root dir /var/www/www.zombie.dnsdojo.org -> /var/www/clients/client1/web1/web/.
web/ contained all of my wordpress files and the index.php and .htaccess files. What I did is go to the WordPress Admin panel and make sure that the WordPress address and Blog address were correct. Since my root domain is also http://www.zombie.dnsdojo.org, the site address wasn't changing. I also went into Misc and checked the permalinks address - still http://www.zombie.dnsdojo.org/year/month/content. I then moved all of my wordpress content to /var/www and removed the clients and virtual hosts. This was a mistake, I know, but it's done. I should have left everything else up until I got the site running in root. Also, I accidentally deleted my .htaccess file since 'mv * /var/www' didn't move hidden files.
So I rebuilt the .htaccess files with from the permalinks page, and can currently navigate to the landing page. I can also get into the admin site. However, every one of my links gives me an Object not Found error. Pages, tags, categories, posts - all broken. I can see content on the landing page, even play embedded video, but no navigation.
I've been around and around trying to figure it out, but I'm at a loss. I'm using mysql 5 and have full access to the server. Any suggestions? I was planning on upgrading to 3.0.1, so if this would help in the fix, I'm up for it. Thanks in advance!