Windows 2008 cluster installation can be tricky given the strict security policies of Windows 2008.
Regarding the LDAP, when you enable and save your configuration from CCM, while you get the message that is accepted it is not! You will have to restart from the cluster manager the GUI Server resource.
I would Advise restarting all the EM Components. Again you should do this restart from the cluster administrator utility.
Additionally make sure that you have the latest fixpack for EM that fixes some issues with LDAP.
As for the Web Server, make sure through task manager that you do not have two web server processes running. If this is the case, then please kill them both and try to restart the webserver from the cluster admin utility.
Also make sure that in CCM , the Web Server component (if any) is in an ignore desired state. (the same goes for all EM components assuming that you use the Cluster Admin utility to monitor the status of the services).
As for the SAP, apply the latest fixpack, and try re-installing the client (and server if any) plugins. The usually reside in the installation CD under the CCM folder. Make sure that you read carefully the command prompt window that will come up for any errors while copying the needed files.
After that, run from the machine where Control-M reside the ctmgetcm command.