Ok, I think I've got this sorted with the help of support. The upgrade was trying to create a mysql table that already existed which threw an error, removing 5 .frm files from the mysql folder allowed the upgrade to complete. However then I couldn't start the PMP service because the upgrade removed the server folder from pmp\jre\bin. I copied that folder back into the working directory from my backup and was able to start the service. It all appears to be working now but I was surprised at the errors received.
1) Attempting to create a table that already exists (I'm guessing five tables actually since I was instructed to remove 5 files but I didn't get to the other four)
2) Removing the server folder from pmp\jre\bin
I'm not sure if this was just a peculiarity in upgrading from 8301 to 8400 and if another version wouldn't have had these problems but I would be curious to know if anyone else has encountered something similar.
1) Attempting to create a table that already exists (I'm guessing five tables actually since I was instructed to remove 5 files but I didn't get to the other four)
2) Removing the server folder from pmp\jre\bin
I'm not sure if this was just a peculiarity in upgrading from 8301 to 8400 and if another version wouldn't have had these problems but I would be curious to know if anyone else has encountered something similar.