I read some of the other issues in the queue relating to this issue but none of the mentioned solutions seem to resolve my issue.
The actual message I'm recieving is:
UPGRADE B: Hostmaster STATUS: upgrade completed
UPGRADE B: Simple check if Aegir upgrade is successful
UPGRADE B: FATAL ERROR: Required file /data/disk/o1/aegir/distro/006/sites/o1.server.com/settings.php does not exist
UPGRADE B: FATAL ERROR: Aborting AegirSetupB installer NOW!
UPGRADE A: FATAL ERROR: AegirSetupB installer failed
UPGRADE A: FATAL ERROR: Aborting AegirSetupA installer NOW!
FATAL ERROR: AegirSetupA installer failed
FATAL ERROR: Aborting Octopus installer NOW!
I removed the /opt/tmp/*FAIL files and the auto created additional 00x folders in /data/disk/o1/aegir/distro/ so only the actual hostmaster install directory exists and the previous one but this resulted in the same error.
Another thing I noticed was early in the installation I got error: SQLSTATE  Access denied for user 'o1'@'localhost' (using password: YES) and now that Aegir isn't able to carry out normal tasks.