someone may correct me, but I believe the exhaust systems and the whole tail section is the same. if your mechanically inclined I don't think it would be that hard to change out the stocker for an aftermarket exhaust.
+1 Somes places/websites still have 04-06 but its because they havent updated their sites. In any case that you are not sure, contact the manufactuer of the product you want to purchase and ask them if its compatible. If they say yes and are wrong, its their a$$ and money if something goes wrong with your bike.
A buddy of mine has an '04 and our exhausts look identical. I did a YouTube search for FZ6 exhaust and found several videos with sound bytes of different exhausts. They all sound great and I'd be hard pressed to make a decision on one for me. Not really an issue for me now because of the cost. My kids have become fond of having cheese with their macaroni and I don't want to take that away from them!