Hello Caitlyn Hessell!
I have seen a number of successful MSD upgrades and the key component is to be well prepared. As you correctly pointed out, the most important thing to keep in mind is indeed matching your GUIDs.
I really think you would benefit from a conversation with our professional services team - they are the most qualified people to help you with this upgrade and guarantee a successful and seamless upgrade. With their help you'll be set in no time! Do reach out (email@example.com) , have a first conversation with them and see how they can help!
I have done the "upgrade dance" from Dynamics 2013-2015, then from 2015-2015 update 1, and am now doing the 2015-2016 dance.
Happy to share my experiences with you - is your instance one of those versions? I have only worked on online versions, not any on-prem instances.
As others have pointed out, matching your GUIDs is most important. The migration from 2013 on-premise to 2015 online was the one that we most concerned about. Now that we're online, the upgrades should be much easier. According to Marketo, their recent plug-in is fully compatible with 2016 online and we shouldn't experience any issues.
Kristen Carmean was the Marketo consultant that assisted us with this. She offered invaluable input throughout the migration. Fortunately, she has a lot MSD experience/knowledge.