Welcome to the wonderful joy of Ford ownership.
Have you tried 3.5.1 update? It seemed to have helped some of my issues... specifically the key fobs not working.
I haven't noticed it yet since update.
Previously I used to have to wait up to a minute presses lock/unlock before the car finally responds, this ofcourse like you described happens intermittantly... now it seems to be instantaneous consistently.
Ford Focus 2012 Sedan 303A SEL w/ Winter package
Sterling Grey Metallic - Medium Light Stone Leather