Well I would still look at a fasttrack migration as it would ensure all records have the same GUID across above systems. Fasttrack would also provide a set of validation checks that would be a very good starting point in identifying what Javascript and plugins need to be rewritten.
Ignoring that the things to watch out for:
You need to choose which systems will be master - this will start as your 2011 instance and move eventually to your online instance
Keep your external systems connected to your 2011 instance and sync from there to the online instance (hopefully you aren't updating those systems from CRM but if you are you need to ensure the online 365 instance updates the master (2011) CRM instance and that then updates the external systems.
Then once you've updated all your external interfaces to use the Web Api you can start the final migration to the online instance.
