Your question is a really big one with many considerations. For example, in terms of the authentication the recommended method is shifting from explicit login and trusts to Mappings and Windows Integrated Security. Also, a major shift would be how PI AF is now taking over the role of PI Module Database; how to handle the migration or side-by-side operation of the two systems in sync is a serious consideration. I would strongly recommend you review the document titled "PI Server 2010 SP1 Installation and Upgrade Guide" from the Tech Support Download Center. It walks you through all these steps and tells you where you need to be cautious.
On any of these special cases if you hit a specific technical matter you may want to consider contacting regular Tech Support for the fastest and most efficient resolution.