Munchkin Code for New Website

People will be tracked on both sites. However, their details won't merge unless they've filled out a form on both sites.

Thus, there will be a cliff when you switch. So you might send an email to the house list to get them to click on the tracked link back to the site and tie their new cookie back.

There is documentation and discussions on this as well.

Well, don't really need to send an email.  

Have the new website check if they have a Munchkin tracking cookie.  If they don't, redirect them back to the old site with a special query param that means "please send old cookie value and return to new website." Old site sees param, reads cookie (if there is one), redirects back to new site decorating the URL with the old cookie. New site reads old value, sets cookie accordingly, then loads Munchkin.  Presto, you have copied the cookie. 

http://www.newexample.com --> http://www.oldexample.com?gimme-the-cookie --> http://www.newexample.com?your-cookie-sir=keys:values

A developer with at least intermediate skillz is necessary to make sure you don't end up w/a redirect loop.

This works because the Munchkin tracking cookie is tiny.  If it were a ton of cookie data you couldn't really pass it this way and would have to resort to some other way of getting the users to re-identify themselves.  I'd hate for you to have to do that if you have already associated leads.