The .htaccess file now contains the following:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
Under permalink settings > custom structure I had /%postname% instead of /%postname%/
Hopefully the rest of the problems are just as easy to fix.
