Hi Lisa,
I've done several integrations/Migrations of Marketo and non-marketo instances and it's a large, but doable process if you stay organized, very much like a salesforce migration process. I personally would not recommend running two separate instances unless you have the teams to manage both and are completely ok with your reporting being entirely separate and connected to separate instances and have cleared the dual munchkin code set up with your web team...it's messy. i don't like it pesonally. 🙂
A few tips
1) Be aware of what information you can and cannot migrate--you can't integrate acquisition history, behavioral tracking, etc. this means your reporting in the new instance will basically have to go from your cut over date onwards. Also be aware that when you break the sync between your old marketo and salesforce instnaces, if your old sfdc instance is still being used, your Marketo instance will not have that interim info, which isn't horrible because you'll be migrating on the sfdc side and get info that way, but it sometimes surprises people.
2) Decide on what information you do and do not need to move over, e.g. how far back of emails and templates? images? reports. make an inventory and be prepared to download all of those items for later upload into the new instance. Given that this is an acquisition, you may only want to keep a couple samples for examples of past campaigns. Also be aware that given that you're migrating to a pre-established instance, you'll have to download and re-upload all used images that you want to keep in the new instance from your old.
3) The biggest time suck in the migration is re-doing legacy programs and acqusition. if you're not migrating old programs over then this is easy. Basically you'll have to download the membership from your old programs that you want reporting for, including their program statuses, then upload them to your new database one the databases have been migrated (i actually just upload their email addresses to speed this up, since the leads are already in there) and then do single flow change actions to update program status info AND acquisition info for each member.
4) Be aware of "order of operations" when it comes to re-integrating your databases between salesforce and Marketo (the following example assumes a 1:1 database balance between mkto and salesforce: take some time to clean your database in the old instance (you can do this with sfdc, but i like it better with Marketo. After the sfdc instances have been migrated, first download old lists (unsubscribe, blacklist, etc.) and the entire database in marketo (I do this because i'm paranoied.) Then sync the new SFDC and Marketo together with NOTHING in the new Marketo instance (or else the sync will push in duplicates which would be awful!) Then once that's done, assess the need to upload your old lists--the info from them would already have been brought in by the new sync of the updated salesforce instance.
5) General tip: stay really organized or you run the risk of duplicate work, missing something or even damage to your database. Spreadsheets are your friend--one per area in Marketo and then one for technical set up (cname etc.)
In conclusion, this is a big job and often one that people can't devote their whole days to. You may be better off hiring a consultant to do this for you or at least help manage.
Best of luck!!
Elizabeth