To the best of my knowledge Yamaha never made a "special edition".
They did however produce a limited run of 1600 called the Silver Edition. The only thing special on them is the speedo face plate.
My 2004 Special Edition.
Well, obviously they made a "Special Edition" and you've got the badge to prove it. So, if I read this right we're looking at paint, badge, hard bags and maybe speedo face plate to delineate this bike from any other run of the mill R*?