As Dr. Sohbet Karbuz explains repeatedly on his energy blog, the primary key for DOD is not in switching fuels, but rather, in reducing the amount of fuel that's needed.
Enter the Pratt & Whitney PW8000 turbofan engine. Long in development, its novel use of gears allows it to use 10% less fuel and it brings other costs savings as well. I'm not saying the Air Force's approach is bad. In fact, in an energy security scenario where the US is cut off from its foreign suppliers, it's essential prep work. But there's no debating the merits of more efficient planes (like the 787) and more efficient engines. We've got to keep pushing the efficiency (and conservation) buttons because synth fuels alone are energy intensive to make, and dollar intensive to buy.