It's early days for the 4 valve 5.4L motor yet. Definitely some improvements to be had in cylinder heads down the track. As far as extra cubes go the 5.4 does have some room to move. The 4.6 motors have options for longer stroke cranks and with the 5.4's 29mm taller deck height it should also. Larger bores which is really where you want to increase the size will probably only be viable once the aluminium blocks hit the scene.
Speaking of which check out the last paragraph of this Autoweek article talking about the proposed Ford GT (new GT40).
What will be the first application in the Ford GT—and will migrate to other uses—is an aluminum version of the company’s 5.4-liter dohc V8. The engine, which gets a supercharger to produce at least 500 horsepower in the GT, will be available as a normally aspirated crate motor for sale on the aftermarket. “Anyone who is doing Ford performance racing is going to want to get this block,” says SVT director John Coletti.
Here's the link to the whole article:
5.4L, 32 valves and huffer potential, mmm, thems good apples.