1. You should have $disallowNamesIndex defined as array in setup_options.php. It should be always defined as array; even if it has no values, it should be an empty array (not a completely removed or disabled).
2. In .htaccess, there should be defined this line:
RewriteRule ^([0-9]+)/$ ./index.php?page=$1&mdrw=on
3. Open templates/main_header.html and locate the CSS class' name to edit it. I'm not sure what do you mean. Additionally, you could use your own colors, tables in the header and so on.