Issue number 2 is an expected result I believe, based on the configuration. We separated the system and domain-level archival functionality, but both are still accessible from a system administrator account. For domain level archives you can view these by clicking on that domain from the Manage page and then using the Message Archive Search tab. For system level archives however you'll need to navigate over to Settings>Message Archive Search instead.
If you have a backup of your JSON configuration files from pre-upgrade you can review these to confirm placement of the original archive directories as well. Please don't hesitate to submit a ticket with us on this if you need a hand :-)
Kyle Kerst
IT Coordinator
SmarterTools Inc.
www.smartertools.com