I have heard that the 04-06 was slightly de-tuned to make the RR stand out a little more but not sure on how true that is.

otherwise the engines are identical.

01-03 isn't horribly uncomfortable, It is actual one of the most comfortable split seat SS out there, But yes the 04-06 would be more comfortable.

 

The raised bars on the F4i make it more comfortable to ride. Seats are negligible, your *** is going to be sore on any bike if you ride a long time. I know from 10+ years of riding and 9 different bikes owned. *** gets sore on every one of them. But the bar position can make or break a good bike.