Pistons are different, injectors are different, 03/04 turbo is smaller, ECM is different. 03/04 heads have push-in valve seats and I believe its 04.5+ have machined valveseats. 03/04 have had dropped valve seats if they get hot. I think its pretty common for those guys to swap to a later head...
Mild mods, say intake/exhaust/programmer, an 04.5-07 will pretty much always make more power and be quicker, on account of the turbo and 3rd injection. Now, get into heavy mods (turbo(s), injectors, modded pump/dual pumps, etc.) the 03/04 trucks seem to be a better platform for making big power. To date, I dont believe there has been a later truck over 1000 on fuel, maybe even 900, however I can think of a couple 03/04 trucks off the top of my head that are over 1000 on fuel, due to differences in the ECM I believe