TwoLane,
My understanding was that there is a significant change in the ECM exactly what I can not tell you, but I can say if they were the same my 2 bikes would be much closer in dyno maps. My buddy also has a pumpkin and his bike dyno'd very close to my pumpkin and yet the 05 wasn't even in the ballpark. The reason I say this is that when we dyno'd them they (my 2 bikes) were identical in accessories Rhinehart true duals 2 1/4 baffles, SE Air Kit with K&N filters and Race Tuner.
Now I know no 2 motors are identical and have + / - variances and variables, but mine were so far apart that there has to be some reason for their vast differences.
I had also been told there was a change in valve train, but after looking through the parts books for both 04 / 05 and then 03 they are identical all the way back. by part number but I did not check to see if there were superceeded part numbers.