This should all be possible to solve using ThinApp and a vb-script copying the local config from a local file share. I've implemented quite a few of those..
Have a look at how to copy files in and out of the virtual environment here: http://pubs.vmware.com/thinapp4/help/wwhelp/wwhimpl/js/html/wwhelp.htm?href=scripts_copy_file_example.html
