I have deleted some redirects I had in the htaccess file and that sped up the site and helped some of the redirects back to the home page. The stylesheets also now load as they should. I can now also activate and delete plugins, most of them, anyway.
I still get redirected to the front page for some plugins I try to go to the settings for. I cannot figure out where the auto 404 is coming from. I've even deactivated Askapache Google 404 plugin and I still get taken to the front page when trying to work with some (not all) plugins. Very frustrating!
Guess I'll try turning off plugins one at a time to see if one of them is causing this.