This thread will have all your answers: http://www.myfocuselectric.com/forum/vi ... =14&t=3812
Basically what happens is one or more modules does not go into sleep mode when the car is turned off. Ford in their infinite wisdom designed the car without a way to troubleshoot this in the event that the problem is intermittent. The only way to troubleshoot it is to catch the misbehaving module in the act of not shutting down. This is done by measuring the current draw on the 12V battery 40 minutes after turning the car off. This delay gives everything time to shut down into sleep mode. The ford spec is that there should be no more than a 50mA draw. FWIW mine measures at 20mA. If it's more than 50mA you literally have to start pulling fuses until the current drops to find the bad module.
Simply buying a new battery to "fix" the problem is a waste of money. The new battery may be strong enough to not be drawn to low to start the car for a few months, maybe even a year. However this will ruin the new battery and you will have to prematurely replace it and you will still have the problem. There that's the Reader's Digest version of the thread linked above.
Edit: Depending on your situation, under normal usage for some reason the motorcraft batteries tend to only last about 3 years in the FFE so you may have simply reached the end of life of your battery.