If you open up your wp-config.php file for your multisite set-up there are some constants you can change…
define('DOMAIN_CURRENT_SITE', 'example.com');
define('PATH_CURRENT_SITE', "https://wordpress.stackexchange.com/");
define('SITE_ID_CURRENT_SITE', 1);
define(‘BLOG_ID_CURRENT_SITE’, 1);
1 in this case refers to the ID of the site that should be the default site. You can figure out the ID of each site by going to your Network Admin -> Sites. Click to edit any one of your sites and check the URL. It will look something like this http://example.com/wp-admin/network/site-info.php?id=3
id=3 tells you the site id is 3.
I’m not sure why you might want to reorder them. Here’s an example of redordering sites in the ‘My Sites’ admin bar drop down -> http://wordpress.org/plugins/reorder-my-sites/ It will at least give you an idea of how to reorder the sites.
If you want to really reorder them you can go into your database and edit the wp_blogs table. Adjust the blog_id column. For each value you change remember to make the same change to the blogs.dir directory for static files (blogs.dir/1/files/… should become blogs.dir/2/files… if you change site ID 1 to site ID 2).
You’ll also need to change the table names and there is an option in the options table called ‘wp_1_user_roles’ so you’ll need to change the 1 to whatever new site ID you set.
You’re moving one of your sites out of multisite and into it’s own WordPress instance? You can probably just do an export of the content and reimport it into the new site, move over your media files and be good to go then.