Downlevel Manifests Folder is not present. System component settings will not be gathered.

Using USMT 4.0 for migrating different settings or apps is not always successful.
I had a problem with Network Printer migration. I tried few times and every try was not successful.
USMT Logs examinations show the following message:

"Downlevel Manifests Folder is not present. System component settings will not be gathered."

As you can see from the picture ScanState.exe has been started from UNC path
ex: \\server name\share name\usmt\x86\scanstate.exe c:\DataMig /i:\\server name\share name\usmt\x86\\migapp.xml /i:\\server name\share name\usmt\x86\\miguser.xml

To resolve this issue my testing showed that Scanstate.exe should be executed directly in USMT working folder:
ex: C:\usmt\x86\>scanstate.exe c:\DataMig /i:migapp.xml /i:miguser.xml

or using Map Network Drive
net use x: \\server name\share name\usmt\x86\
x:\scanstate.exe c:\DataMig /i:migapp.xml /i:miguser.xml 

Using this way USMT Scanstate.exe will find a path to the appropriate manifest folders.

Certificates for the default management point are not available (internal error)

This error message appears during creation of Task Sequence Media and choosing Bootable media.

The message 4970 appears on SMS_MP_CONTROL_MANAGER:

Severity    Type    Site code    Date / Time    System    Component    Message ID    Description
Error    Detail        11/2/2012 10:42:45 AM    SCCM    SMS_MP_CONTROL_MANAGER    4970    SMS Site Component Manager faild to install component SMS_MP_CONTROL_MANAGER on server SCCM.    The WebDAV server extension is either not installed or not configured properly.  Solution: Make sure WebDAV is installed and enabled. Make sure there is an authoring rule that allow "All users" read access to "All content". Make sure the WebDAV settings "Allow anonymous property queries" and "Allow property queries with infinite depth" are set to "true" and "Allow Custom Properties" is set to false.

Solution for this issue is:

Enable WebDAV on Default Web Site on IIS.

Add Authoring Rule  and configure the settings based in the picture.

Edit WebDAV settings and configure them and click Apply.

Enable Communictaion settings on ConfgMgr Distribution point Properties.
 
http://technet.microsoft.com/en-us/library/cc431377.aspx