removing index.php messing up site
I just did an install last week and had no problems, but it was a different server.
1) You should be able to access any page by manually typing index.php as the first part of the path of the url, e.g.www.www.example.com//index.php/dashboard/.... Assuming you can, try clearing and disabling the cache - particularly if full page caching is enabled.
2) Has the .htaccess file actually been written or uploaded to the site's document root?
3) Does this server actually support mod_rewrite?
4) Does this server allow the processing of .htaccess files? An easy way to find out is to replace .htaccess with some other text file containing any old rubbish. If it is processing them, you should receive a 500 server error because the file will now have incorrect information in it.