After one week I recieved my 2013 Ford Fiesta back today from Ford. Both inner input shaft seals and the clutch were replaced. The PCM/TCM were also reprogrammed. The car was still under warranty from Ford so I had no out of pocket expense. The car runs fine now.
I spoke with the GM of Findlay Honda who sold me the car and he was very understanding to the frustration I was experiencing throughout this process. He offered to help me if needed and was very respectful. I commend Findlay Honda on their customer service in this less than perfect situation.