03 is the first year that they came with fuel injection.
They were all the same model from 03 - 05 with a couple small changes.

In 05 they inverted the forks and the engine came with an extra 3 hp. And the intake box recieved 2 different length velocity stacks.

Then in 06 they changed everything. So the 06 - 09 is the same bike. It is commonly known as the R6r.

They also offered an R6s model from 06 - 09, which is the same model from 03 - 05. It did recieve the new engine set up and intake. But did not get the inverted forks.

So... if you have an 05. It is the same as my 06 R6s except you have the inverted forks and I dont.