If you “removed WP by FTP” you will need to reupload the WordPress files. See Uploading WordPress to a remote host.
Once you’ve uploaded the files and can access your blog, then try updating your permalinks via Administration > Options > Permalinks.
No, that didn’t really help. I’m using WordPress with Joomla and I had my website all set up prior to installing WP. I actually had a previous version installed and updated to 2.3.1. When I did that it broke all the links from my index page on the website to the internal pages. None of the other pages of my website are accessible. The blog is fine. But for some odd reason, when I click on a link on my menu bar at the website I end up on the blog’s 404 page. When I remove the WordPress files and take the blog completely off the website, all I get is a 500 error page. Oddest thing I’ve ever seen.
