I've been looking into buying a '03 4.6is myself. It's got 90K on it so I've been doing my research. Those more knowledgeable please correct or add but this is what I've found so far.

There are many problems with the transmissions. Apparently the place to get new ones are from Level 10 http://www.levelten.com/default.asp or Autosports unlimited http://www.autosportsunlimited.com/index.html

There seem to be several problems with the air suspension leaking or failing. Not sure on the easy fixes for that; however, there are places that rebuild the air shocks for less than OEM.

The window regulators seem to come up as issues on this board quite frequently too.

Other things I've noticed are the valley pan gaskets, valve cover gaskets, the oil separator on the back of the manifold and the aluminum coolant tubes rusting / leaking under the manifold.