The jts/setup for CLM 4.0.1.0 went well until the "Finalize Setup" under "LIFECYCLE PROJECT ADMINISTRATION (/admin) setion". The "Link Applications" failed with the following message (Please note, I can login jts/admin, ccm/admin, qm/admin, admin/web and rm/web but certainly with missing CLM application links))
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Platform: Linux X64 (RHEL 5.8)
Proxy Server: IBM HTTPS x64 8.0.3 (host1)
AppServer: WAS 8.0.3 X64 (host2)
Database Server: DB2 V9.7 FP6  (host3)
LDAP Server: MS AD on W2K3 X86
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CRJCA0003E The Lifecycle Project Administration (LPA) application made a request that was answered by an unexpected response code. The request was: https://<reverse-proxy-hostname>/qm/service/com.ibm.team.repository.service.internal.discovery.IFriendsAdminRestService/newFriend. The response was: HTTP/1.1 500 Internal Server Error. For more details, open the help system and search for CRJCA0003E.

The admin.log shows:

2012-12-09 17:00:20,633 [                     Thread-90]  WARN com.ibm.team.lpa.http                     

         - CRJCA0042W Host https://<reverse-proxy-hostname> has indicated a problem with an LPA request.

>>> POST https://<reverse-proxy-hostname>/jts/proxy?uri=https%3A%2F%2F<reverse-proxy-hostname>%2Fqm%2Fservice%2Fcom.ibm.team.repository.service.internal.discovery.IFriendsAdminRestService%2FnewFriend HTTP/1.1

>>> X-Requested-With: JazzHttpClient

>>> X-socket-timeout: 1200

>>> X-jazz-downstream-auth-client-level: 4.0

>>> X-jazz-proxy-chained-callback: https://<reverse-proxy-hostname>/admin/oauthCallback

rootServices=https%3A%2F%2F<reverse-proxy-hostname>%2Frm%2Frootservices&oauthConsumerKey=2de63e215b0140728d1f91b8f24bb4f1&title=Requirements+Management+%28%2Frm%29&internal=false&oauthConsumerSecret=eNxSsVeYdejdOCJo0jYYfyVOx%2BQ8FsZhjE%2FL27EvTBY%3D

<<< HTTP/1.1 500 Internal Server Error

<<< Date: Sun, 09 Dec 2012 22:00:20 GMT

<<< Server: IBM_HTTP_Server

<<< X-Powered-By: Servlet/3.0

<<< $WSEP:

<<< Content-Length: 221

<<< Connection: close

<<< Content-Type: text/html;charset=UTF-8

<<< Content-Language: en-US

Error 500: org.eclipse.core.runtime.AssertionFailedException: null argument:The local application&#39;s root services could not be fetched, contained invalid content, or was missing the required entry for jfs:oauthDomain

2012-12-09 17:00:20,736 [                     Thread-90] ERROR com.ibm.team.lpa.config                             -

com.ibm.team.lpa.automation.TaskException: CRJCA0003E The Lifecycle Project Administration (LPA) application made a request that was answered by an unexpected response code. The request was: https://<reverse-proxy-hostname>/qm/service/com.ibm.team.repository.service.internal.discovery.IFriendsAdminRestService/newFriend. The response was: HTTP/1.1 500 Internal Server Error. For more details, open the help system and search for CRJCA0003E.

        at com.ibm.team.lpa.common.tasks.AbstractTask.handleError(AbstractTask.java:145)

        at com.ibm.team.lpa.common.tasks.CreateFriendTask.runTask(CreateFriendTask.java:91)

        at com.ibm.team.lpa.common.tasks.AbstractTask.run(AbstractTask.java:56)

        at com.ibm.team.lpa.automation.CompositeTask.run(CompositeTask.java:208)

        at com.ibm.team.lpa.common.tasks.AbstractCompositeTask.run(AbstractCompositeTask.java:25)

        at com.ibm.team.lpa.automation.CompositeTask.run(CompositeTask.java:208)

        at com.ibm.team.lpa.automation.CompositeTask$MonitoredSubTask.run(CompositeTask.java:124)

        at com.ibm.team.lpa.automation.CompositeTask.run(CompositeTask.java:208)

        at com.ibm.team.lpa.common.tasks.LoggingCompositeTask.run(LoggingCompositeTask.java:37)

        at com.ibm.team.lpa.automation.AsyncTask$TaskRunner.run(AsyncTask.java:40)

       at java.lang.Thread.run(Thread.java:769)

2012-12-09 17:00:20,736 [                     Thread-90] ERROR com.ibm.team.lpa.config                             - Server response: Error 500: org.eclipse.core.runtime.AssertionFailedException: null argument:The local application&#39;s root services could not be fetched, contained invalid content, or was missing the required entry for jfs:oauthDomain