Remove everything except the user-uploaded files (I think it will be /uploads, as well as /gallery and/or /blog if you have them). (I wouldn't be sure of the file names though).
Also keep conf_global.php. (Make sure you back everything up first.)
Then just upload the files for a clean 3.0.1 install, go to /admin/upgrade and follow the prompts.
Also, if you're not comfortable doing this, IPS can do the upgrade for you. Submit a ticket about it.