The 04-06 FZ6s have different front fairings/cowlings than the 07-09s, but they have the same tail section/rear side pods. That being said, you could interchange the two of the front cowlings no problem, but the issue arises with the speedometer.
The 04-06s have a roundish full digital speedo and the 07-09s have a more rectangular analog tach/digital speedo unit. So if you put the 07 front cowling on your 05, it would fit, but the hole for the speedo for the 07 fairing wouldn't fit your 05 speedo. Does that make sense?
You could always get an 07 speedo to fit the hole (of course you'd have a different mileage number) or just cut the newer fairing out a little if you had to/fill the hole with other stuff (you could install a gear indicator or a 12v cigarette lighter socket or toggle switches for heated grips, etc.). Also, you MAY have to get the newer fairing stay to mount up the newer front cowling, but I'm not sure. There is a member on here who switched to newer style fairing, so try doing some searching and I'm sure you could find the answer on that.
The lower cowling/belly pans should be universal across all years, BUT if you wanted to get full fairings, you'd have to get the correct ones for your bike. However, if you switched to the 07 fairing and decided to put full fairings on the bike, you'd need to get 07 full fairings.
