It appears that iismt doesn't cannot do this.
Internet Information Services 6.0 Migration Tool version 1.1
Copyright (C) 2002 Microsoft Corporation. All rights reserved.
Connecting to the local IIS Server...
Connecting to server ftp1...
Resolving the site by name 'LM/MSFTPSVC1/1'...
The IIS Migration Tool cannot find the specified site
I tried both MSFTPSVC/1 and "Default FTP Site" all with the same results. Is there anything I can do? There's over 100 virtual directories along sophisticated NTFS permissions.