Re: what is the difference between them
I have rode the 2004 and the 2006 models (and the 'new' 2008 model). The 2004 1000RR is an excellent bike to own & ride every day but the press (UK magazine reviews) slated it for being too tame (and I must say that I was not very impressed with the acceleration or ability to drop into corners).
The main difference to the 2006 version is the gearing ratio's; so some 2004 / 2005 model owners changed the sprockets to give it a bit more acceleration.
There were quite a few more minor mods also but can't remember the details.
It is an excellent bike and if you are happy then keep it as it is but I would recommend putting a smaller -1 tooth sprocket on the front or changing the rear sprocket to a +2 or +3.