I have made the necessary changes and have chls up and running between my config mgr and broker. When I deploy, I now get these errors:

BIP2066E: Broker LINUX3 (UUID 2c6ffcc4-0401-0000-0080-8258071abfb5) was unable to retrieve an internal configuration response message for execution group '$SYS_mqsi' within the 360 second Configuration Timeout.

The execution group did not respond within the Configuration Timeout period. A negative response is returned to the Configuration Manager for this execution group. The Configuration Timeout is the maximum length of time that an execution group is allowed to apply a deployed configuration change. By default the Configuration Timeout period is 300 seconds. You can increase (or decrease) the timeout by using the mqsichangebroker option, ConfigurationTimeout. This will not resolve any underlying problem with the deployed message, but can be used to reduce the response turnaround time or increase it to allow for large and complex deployments.

Investigate why the execution group was unable to respond before being timed out. Use the system log messages to determine if there is a problem with the execution group. You should check that your system is not running short of resources, for example, you may need to increase the WebSphere MQ log size. Reducing the complexity of the deploy by reducing the number of execution groups may also help to alleviate this problem. Correct the problem and redeploy the broker's configuration from the Message Brokers Toolkit. If there are no other failure diagnostics then you should consider increasing the Configuration Timeout, increase this value in units of 300 until this message no longer occurs. Contact your IBM support center if you are unable to resolve the problem.

BIP1536S: Configuration Manager unable to register for internal subscriptions with broker LINUX3.

Although the preceding deploy operation was successful, a subsequent attempt by the Configuration Manager to register for internal subscriptions with broker LINUX3 was not successful. This means that the Message Brokers Toolkit may not reliably show the correct status of the resources assigned to broker LINUX3. The Configuration Manager also writes this message to the system event log, accompanied by other messages giving details of the problem.

Look at the messages for this problem in the system event log. Determine and correct the cause of the problem before attempting to deploy to this broker again. If this problem persists, contact your IBM support center.

And in /var/log/messages:
Jun 28 19:02:43 localhost MQSIv500[3587]: (LINUX3)[32771]BIP2811E: The broker was unable to receive a 'stopped' publish event response. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 670: ImbAdminAgent::monitorAdminAgentParentProcess: :
Jun 28 19:02:45 localhost MQSIv500[3567]: (LINUX3)[16384]BIP2002W: The WebSphere Business Integration Message Brokers service has stopped. : LINUX3.service: /build/S500_P/src/AdminAgent/ControlProcess/Linux/ImbControlService.cpp: 522: ImbControlService::CleanUp: :
Jun 28 19:02:58 localhost MQSIv500[4647]: (LINUX3)[16384]BIP2001I: The WebSphere Business Integration Message Brokers service has started, process ID 4650. : LINUX3.service: /build/S500_P/src/AdminAgent/ControlProcess/Linux/ImbControlService.cpp: 342: ImbControlService::StartNewAA: :
Jun 28 19:03:00 localhost MQSIv500[4666]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4666'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:01 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4666, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:01 localhost MQSIv500[4669]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4669'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:02 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4669, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:03 localhost MQSIv500[4674]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4674'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:03 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4674, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:03 localhost MQSIv500[4679]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4679'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:04 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4679, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:05 localhost MQSIv500[4684]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4684'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:05 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4684, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:06 localhost MQSIv500[4689]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4689'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:07 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4689, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:07 localhost MQSIv500[4695]: (LINUX3.$SYS_mqsi)[16384]BIP2201I: Execution Group started: process '4695'; thread '16384'; additional information: brokerName 'LINUX3'; executionGroupUUID '82a6e590-12b3-11d3-81a2-00203506a68e'; executionGroupLabel '$SYS_mqsi'; defaultExecutionGroup 'true'; queueManagerName 'LINUX3'; trusted 'false'; dataSourceName 'LINUX3'; userId 'db2inst1'; migrationNeeded 'false'; brokerUUID '2c6ffcc4-0401-0000-0080-8258071abfb5'; filePath '/opt/mqsi'; workPath '/var/mqsi'. : LINUX3.82a6e590-12b3-11d3-81a2-00203506a68e: /build/S500_P/src/DataFlowEngine/ImbMain.cpp: 235: main: :
Jun 28 19:03:08 localhost MQSIv500[4665]: (LINUX3)[65541]BIP2060W: The broker has detected that the Execution Group $SYS_mqsi, process ID 4695, has shutdown. : LINUX3.agent: /build/S500_P/src/AdminAgent/ImbAdminAgent.cpp: 3876: ImbAdminAgent::startAndMonitorADataFlowEngine: :
Jun 28 19:03:19 localhost kernel: application bug: bipservice(4651) has SIGCHLD set to SIG_IGN but calls wait().
Jun 28 19:03:19 localhost kernel: (see the NOTES section of 'man 2 wait'). Workaround activated.
Jun 28 19:04:19 localhost kernel: application bug: bipservice(4651) has SIGCHLD set to SIG_IGN but calls wait().
Jun 28 19:04:19 localhost kernel: (see the NOTES section of 'man 2 wait'). Workaround activated.
Jun 28 19:05:20 localhost kernel: application bug: bipservice(4651) has SIGCHLD set to SIG_IGN but calls wait().
Jun 28 19:05:20 localhost kernel: (see the NOTES section of 'man 2 wait'). Workaround activated.