Unfortunately it's one of the last Mondeos that did not have USB as standard even with the premium audio option selected :'(
As far as conversion goes, yeah, I use gnome soundconverter all the time to get OGGs from FLACs
-BUT-
being a bit of a free software vegan I like to avoid MP3 whenever possible. It's a purism thing, not a technical challenge. Yeah, I'm a weirdo.
But since the Ford USB module doesn't sound too good to begin with, I'll probably be sticking with a nice PMP plugged into the aux jack. Having functional steering wheel controls would be nice, the most important ones (volume) still work though.