The name servers are pointing to the new Linux machine from now on, and things are running smooth (so far).
The WordPress database issue was solved by upgrading to the latest 2.3.1 version, which required a DB upgrade anyway, and fixed the tables that where incorrect. I had manually fix the md5 hash codes for the passwords, but since only a few users have accounts here, that wasn’t a problem.
I have nice permalinks up again now, without that index.php thing in them even, so that’s even better than before. I’m using Dean’s Permalink Migration plugin to make sure old links from all over are still working, and not loose too much Google rank etc, though I doubt that all those http errors from the Windows machine did a lot of good for that.
While I’m at it, here’s a tip if you plan to migrate a WordPress installation any time soon. Then you’ve restored a database backup on a new system, the first thing to do is adjust the blog and site URL to the new location. While you’re at it, change the blog title as well.
WordPress has a habit of using those URLs a lot in redirects, and if you forgot to change those, you’ll end up being swung over to the site your backup is from. If you didn’t change your blog title there’s a big chance you won’t notice you’re now working on the live site, and might end up screwing things up.
Which ain’t fun.
You can find and change these parameters in your mySQL database in the wp_options table with the values (option_value) “home“, “siteurl” and “blogname“.