Firstly I'd suggest transferring your lead scoring system over to the new Marketo instance. If you have this system set up within a single Program, this should be relatively pain-free. Simply send a ticket to Marketo Support to request this Program to be moved across, and they should be able to help.
Then, simply download the complete database from your existing Marketo instance, and re-import this into the new instance, taking care to map the fields correctly (and creating any new custom fields if required). As long as you map the scoring fields correctly, this should migrate well, although keep in mind that it will most likely take several hours to complete (but you don't need to stay logged in, thankfully!).
One thing I can think of that you'll need to look out for when changing Marketo instance would be to make sure you get your IT setup done properly again, as you'll now have a new account string and Munchkin code to handle.
Good luck with it, and let us know if you notice any more hurdles or pitfalls along the way!