As Joe stated there is a difference in how the headers come out of the motor. The 05 left side header comes out and makes a pretty sharp U turn and then goes to the collector. Another difference on the exhuast is the muffler, the 05 utilizes a straight type of connector to the collector, where the 04 has the older KTM design that kind of looks like a ball and socket type connection.
The 05 also has a kickstarter that wraps around the collector. The 05 also has a thermostat in the cooling system that is clearly visible on the left side, that has a small bypass hose in line as well. The 05 also has the smaller eliptical type of odometer. Some small graphic changes as well but essentially the same dimensions on the tank seat.