I forgot about my newer side panels. They are white and think from 05 or 06. I also had to do some grinding to get the panels to mate to the 01 subframe rails.
D251Man,
I would guess the 01 side panels would bolt up much easier than we had to do. The 01 panels have a flater profile on the inside and should mate up to your 04 bike easier. Not sure on the air box cover though... mine is also an 01 cover with my newer side panels. I would think the fenders would bolt on with maybe minor tweaks to the rear fender. However, it sounds like the shrouds will be an issue.