The "no cfg structure..." issue generally hits you before you ever do the actual upgrade - it prevents successful transfer of the new image onto the target ASA's flash (disk0:).
I've upgraded dozens of firewalls and never had one fail to boot and/or become inaccessible. Where I've encountered issues has generally been around fine tuning some NAT rules or access-lists after the parser translates the pre-8.3 commands.
If you have Cisco Smartnet support you can always open a proactive TAC case to request assistance.