This worked for me, give it a shot:
Trying to return the vehicle to stock in the normal manner will fail, but I can return it to stock tune by: trying to again download a custom tune, turning the key off as it updates (resulting in a download error), the tuner asks to return to stock, I accept and the update works successfully. The car will then start, on the stock tune.
Mine: 2002 Focus SVT: 142k, Sonic Blue, #1654, All Options
Mods: Tom's Tune, Borla, HFC, STS, Painted Machs, Euro Grill, FRPP Springs
Hers: 2010 Focus SES: 67k, Ebony, Auto, Moon and Tune