It is somewhat known that the SVT can be problematic to tune. If you search around you'll find others who have had issues tuning them; and others have worked flawlessly. No one, that is Tom or any of the staff at SCT, can tell you if your car will be problematic before tuning is attempted. Really wish someone was able to because it would save a lot of headache.
Now that you, and we, know your car is a problem child, it is in your best interest to contact SCT and see if they are willing to help. Tom has limited capabilities in comparison. SCT may be able to update or repair the Xcal via specific updates or remotely connecting to your PC and adjusting the Xcal (not your car).
I do know of instances where they were able to repair the device W/O sending it in and only took an hour or so.
FWIW, the reason the SVT has issues while the other Focus's don't is that the SVT uses a different style of ECU from a different manufacturer. The problems aren't limited to just the Focus either, it's the entire SVT lineup being all of them use ECU's from the same supplier.
Anyways, take the time to calm down and call for help. Odds are it'll work out and things will all fall into place and work as they should.
121,000 members and still no sponsored racing.