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It is a really good idea to uninstall the previous version and then install the new one, at least and especially when changing major version numbers. So if you didn't do a clean install of your first 3.x version, now would be a good time.
Unless you select the option to delete all directories during the uninstall, your settings, bookmarks, and add-ons will be preserved.
If problems persist, it's a good idea to test the browser in Safe mode, by starting it from the Safe Mode option in the Windows Start menu. Problems with incompatible add-ons can be isolated that way.
I did an uninstall and a clean re-install of 3.0.4 as suggested. I'll have to report back on any further difficulties.
I'm assuming that it is some issues with my plug-ins, but I just haven't had time to sit down and troubleshoot.