I've got a 2010 with the 5.4L and 365,000km. I've done all the breaks recently, calipers, rotors, pads.
I've bleed the breaks several times and there's no more air in any of the lines. Also replaced the master cylinder as a last ditch effort, and the breaks still feel spongy!! There's no leaks anywhere in the system I can see. Anyone no something else I should be looking at or is this just how they are??

 

With those type of repairs it's required that an electronic service bleed be performed to remove trapped air in the HCU for the brake system. There's a couple ways of doing that. If your pc savvy and have a Windows laptop/tablet you can d/l a free program called Forscan and buy a cheap obd2/usb pass thru cable off Amazon and perform said service bleed yourself or head to your local Ford service department and pay them to do it.

You'll never get a good pedal until this procedure is performed.