I haven't tried the manual method yet, because I'm still not sure if the problem is with the plug-ins or the hard code of the site and would like to be sure before I do something stupid (or something I'll just have to redo later...).
This issue began with WP-Stats and it's little "lets redirect you to your own website" loop error that everyone was having (and has yet to be fixed? not sure about that) and has now extended to anything update-able on my site. Now, whenever I go to update something, it just redirects me to my website's 404. I can't seem to find anything else about this on the forum, and my apologies if I've overlooked it, but does anyone have any idea what is going on?