Below are few troubleshooting tips for CRA subsystem problem.
Checkout the below URL which address JTAPI subsystem startup problems
http://www.cisco.com/en/US/products/sw/voicesw/ps556/products_tech_note09186a0080154fcd.shtml
For RM-CM Subsystem,
Symptom:- The Resource Manager Contact Manager (RM-CM) subsystem is out of service.
Possible Cause The RM JTAPI user in Cisco allManager is not configured properly.
Recommended Action
1. From the CRA Administration web page, choose Subsystems > ICD, click the RM JTAPI Provider hyperlink, and then make sure that the information
in the RM JTAPI User ID and Password fields matches the information for the RM JTAPI user in Cisco CallManager.
2. In Cisco CallManager, verify that the Enable CTI Use option is enabled for the RM JTAPI user.
3. Make sure you have associated the agents phone to the user.
For Database Subsystem, check if you have configured the DSN Properly.
For Email Subsystem, check if you have configured the email subsystem properly.
Take a look at the below URL which explains how to configure various subsystems in CRS.
http://www.cisco.com/univercd/cc/td/doc/product/voice/sw_ap_to/apps_3_1/english/admn_app/cra_adm/submenu.htm
I'm not getting your second question? What do you mean by "they not installed during original install"?
Regards
Venkat