I would have pushed for the new parts, but that's it. Additional amounts of money back and a free extended warranty is excessive. Last I knew a 100K exteneded warranty was worth about $1800 or more.
Unfortunately you can cut off your nose to spite your face. Now you don't have the car you wanted and that damage could have easily happened later on driving down the road. So this is kind of a no win situation.
I live in the south bay area too. If you are going to attempt to order again for a 2014, I would recommend The Ford Store in Morgan Hill. They are excellent and always discount off the MSRP. No mark-ups. PM me if interested and I will give you the name of a no-nonsense premier salesperson there who knows and drives performance cars. Perhaps they could even find you a 2013.
And no, I don't work for them. Just a happy customer with both sales and service.