@Jonathan Hurley Sorry for the late reply but based on your lead I was able to figure out the root cause of my issue.
When I pulled the logs you mentioned I found the following:
2016-09-06 20:44:23,410 - Backing up /etc/hadoop/conf to /etc/hadoop/conf.backup if destination doesn't exist already.
2016-09-06 20:44:23,411 - Execute[('cp', '-R', '-p', '/etc/hadoop/conf', '/etc/hadoop/conf.backup')] {'not_if': 'test -e /etc/hadoop/conf.backup', 'sudo': True}
2016-09-06 20:44:23,436 - Checking if need to create versioned conf dir /etc/hadoop/2.5.0.0-1245/0
2016-09-06 20:44:23,438 - call[('ambari-python-wrap', u'/usr/bin/conf-select', 'dry-run-create', '--package', 'hadoop', '--stack-version', u'2.5.0.0-1245', '--conf-version', '0')] {'logoutput': False, 'sudo': True, 'quiet': False, 'stderr': -1}
2016-09-06 20:44:23,466 - call returned (1, '', "Sorry, user ambari is not allowed to execute '/bin/ambari-python-wrap /usr/bin/conf-select dry-run-create --package hadoop --stack-version 2.5.0.0-1245 --conf-version 0' as root on myserver.mydomain.com.")
2016-09-06 20:44:23,466 - Package hadoop will have new conf directories:
2016-09-06 20:44:23,468 - Checking if need to create versioned conf dir /etc/hadoop/2.5.0.0-1245/0
2016-09-06 20:44:23,470 - call[('ambari-python-wrap', u'/usr/bin/conf-select', 'create-conf-dir', '--package', 'hadoop', '--stack-version', u'2.5.0.0-1245', '--conf-version', '0')] {'logoutput': False, 'sudo': True, 'quiet': False, 'stderr': -1}
2016-09-06 20:44:23,496 - call returned (1, '', "Sorry, user ambari is not allowed to execute '/bin/ambari-python-wrap /usr/bin/conf-select create-conf-dir --package hadoop --stack-version 2.5.0.0-1245 --conf-version 0' as root on myserver.mydomain.com.")
2016-09-06 20:44:23,496 - checked_call[('ambari-python-wrap', u'/usr/bin/conf-select', 'set-conf-dir', '--package', 'hadoop', '--stack-version', u'2.5.0.0-1245', '--conf-version', '0')] {'logoutput': False, 'sudo': True, 'quiet': False}
2016-09-06 20:44:23,524 - Could not select the directory for package hadoop. Error: Execution of 'ambari-python-wrap /usr/bin/conf-select set-conf-dir --package hadoop --stack-version 2.5.0.0-1245 --conf-version 0' returned 1. Sorry, user ambari is not allowed to execute '/bin/ambari-python-wrap /usr/bin/conf-select set-conf-dir --package hadoop --stack-version 2.5.0.0-1245 --conf-version 0' as root on myserver.mydomain.com.
2016-09-06 20:44:23,524 - Directory['/etc/hadoop/conf'] {'action': ['delete']}
2016-09-06 20:44:23,563 - Removing directory Directory['/etc/hadoop/conf'] and all its content
2016-09-06 20:44:23,593 - Link['/etc/hadoop/conf'] {'to': '/usr/hdp/current/hadoop-client/conf'}
2016-09-06 20:44:23,862 - Warning: linking to nonexistent location /usr/hdp/current/hadoop-client/conf
2016-09-06 20:44:23,862 - Creating symbolic Link['/etc/hadoop/conf'] to /usr/hdp/current/hadoop-client/confIn particular, one line that stood out:
2016-09-06 20:44:23,466 - call returned (1, '', "Sorry, user ambari is not allowed to execute '/bin/ambari-python-wrap /usr/bin/conf-select dry-run-create --package hadoop --stack-version 2.5.0.0-1245 --conf-version 0' as root on myserver.mydomain.com.")
In my instance of HDP, I choose to run Ambari-Agent under a non-root user account called 'ambari' with sudoers permissions. I based my sudoers file off of the documentation found here:
https://docs.hortonworks.com/HDPDocuments/Ambari-2.2.0.0/bk_Ambari_Security_Guide/content/_how_to_co...
What I didn't have included was '/bin/ambari-python-wrap' in the list of approved commands. After adding that and recreating the cluster, all of my issues were resolved. So if anyone is having similar issues in HDP-2.5.0 and is running Ambari-Agent under a non-root user account, make sure '/bin/ambari-python-wrap' is listed under your commands section in your sudoers file.
