I checked out the code, but in the end I finally found it. I started eliminating posts one by one and there was one post that was corrupting the whole page. I eliminated that post and recreated it and everything was fine. Thanks for your help.
I set it back to the default theme, it’s better but still messed up. My sidebar goes to the bottom of the page on page 2. Like before, page 1 is ok, but page 2 and beyond is still a mess.
I don’t know what I did… I only changed the index.php and .htaccess. Is there a way to just save everything back up the database and then uninstall and reinstall wordpress to the root?
I was able to go into the MyPHPAdmin and update the site URL directly in there.