Actually, in 2004.5 they introduced the LLY with VVT. Higher performance and lower mpg's.
They also beefed up the block in 2006. The accessories also have changed since 2001. I think 2006 the allison got a 6th gear.
But, you can take a 2008 short block and bolt on heads and all accessories from a 2001. You can swap cranks, pistons, rods and intake manifolds between the two. Obviously, the newer stuff is improved with ongoing engineering.
In 2003 Ford had the 7.3, then the 6.0, the 6.4 and will have the 6.7 in 2009. That's 4 totally different engine designs in 6 model years! You won't find much interchange between any of those 4 engine families, maybe the paint.... Those engine changes are way different than the 221 v8 changing into the 260, the 289, the 302, the way stupid 255, the 5.0L with actual displacement of 4.9l), the 351w, the 5.8l. There is less interchange between those engines of the same family than between the duramax of 2001 and 2008.