Hmm, unless you've got a very understanding dealership or they can find a part that actually failed in the motor, your warranty is gone. More than likely I wouldn't be expecting a call from ford saying they will warranty the engine if you installed it yourself. The 12month/12K warranty is usually only good on parts installed by them.
I had a car I worked on that had a clutch go bad after installing all new ford parts. It was actually caused by a bad master cylinder, but still couldn't get a warranty on the parts.
Sorry,
Rick
