This was a painless upgrade but I found two quirks,
1) when you edit your config.php then you must set the chmod permissions to 600. If you try 400 then the Pandora Console still thinks that the file is readable by others. Obviously a bug but nothing to worry about. Note that to edit the ./include/config.php you must copy the new version 5 ./include/config.inc.php to ./include/config.php and then edit that new config.php and copy and paste in your custom settings from your old version 4 config.php file.
2) The ./extras/pandoradb_migrate_4.0.x_to_5.0.mysql.sql (and actually any of those migration files) is missing a schema change to the tagente_estado table. It has,
ALTER TABLE `tagente_estado` ADD COLUMN `last_known_status` tinyint(4) NOT NULL DEFAULT 0;
but ALSO needs to have,
ALTER TABLE `tagente_estado` ADD COLUMN `last_error` tinyint(4) NOT NULL DEFAULT 0;
else the pandora_server won’t start.