How can I reconfigure the Performance Analysis SQL Server if the port for repository database wil (46605)

How do you change the PA SQL Server repository settings to accept a change of SQL Server ports being used?

You have to modify two files:

1) database server:
        - Go to <install dir>\agents\SC_MSSQL\6.0\<hostname-instance>\quest_sc_collector\config\
        - Make a backup copy of the file sc_repository
        - Open the file and modify the line:  
               port "1433"
            to
              port "3500"

2) middleware server:
        - Go to <install dir>\agents\SC_MSSQL\6.0\<hostname-instance>\quest_sc_rep\config\
        - Make a backup copy of the file sc_rep_mngr.xml
        - Open the file and modifiy the port in the following tag:
              <target_db_config sid="<instance name>" host="<host name>" port="1433" user="sa" db_name="Quest_Performance_Repository" db_type="1"
                  password="46b8861a72258ce1" tns_entry="" authentication="0"/>
            to
              <target_db_config sid="<instance name>" host="<host name>" port="3500" user="sa" db_name="Quest_Performance_Repository" db_type="1"
                  password="46b8861a72258ce1" tns_entry="" authentication="0"/>  

        - This tag should appear two times. NOTE: modify only the tags for the target_db not for the source_db!

Before you will do the changes stop Performance Analysis and restart it after you finish the changes.