I think I figured out the permissions error. I had to grant the Web Service account ‘Traverse Folder / Execute File”, “List Folder / Read Data”, “Read Attributes”, “Read Extended Attributes”, “Read Permissions” on the installation bin folder of SSNS.
Now I noticed that somehow my NS$BamAlerts service is not running. I am looking into that now. I believe I just need to register the service again using Notification Svs command prompt. Then I should be able to edit the biztalk config file to point to the cluster server name.