Is your TimeFactor in update mode? If you put the TimeFactor in update mode, then I assume the updater will find it. You'll want to turn the TimeFactor off and then on again with the middle footswitch pressed to put it in update mode, and then open the updater.
The kind of problem that you've described — where the update fails in the middle — almost always can be fixed by updating the software responsible for performing the updates first and then applying the update. I walked another user through that process in this forum thread: http://forum.eventide.com/cs/forums/t/9492.aspx. Do you have access to a Windows PC? Because it would be preferable to try this process with the Windows application I posted on that other thread. But if you don't, the same basic process can be done on Mac with the update software that you've already been using. Let me know if you'd like instructions for doing this on Mac and if the updating software on Mac now finds your stompbox after booting it into update mode.