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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!
Thanks Adam. I'm aware of the munckin code. What do you mean by account string?
We already have our two new production environments linked together--although they're empty right now: SFDC Production to MKTO Production
The Account String is unique to each Marketo instance, found in Admin > Landing Pages and is used for setting up branded tracking links & landing page URLs. Now that you have a new instance, and (I assume) a new Account String, you'll need to get your IT department to make the relevant DNS changes on your domain to take this into account.
These DNS changes should be relatively simple to update, but it's best to be aware of and put in your schedule early on to avoid confusion later!