I took my 1300 in for its 600 mile service (an American bike) to my local Yamaha dealership here in Canada. When I talked to the service guy about the whine, he said Yamaha Canada is actually paying to have all the clutch baskets replaced in the Canadian 1300's which gets rid of (or tones down) the whine...he says it's different for different bikes, but can really mess up your bike if it gets out of hand.
I phoned Yamaha USA and they are aware of what they call a "drive line noise". They aren't replacing the clutch basket, but they say they have a couple of options that a dealership's regional rep will suggest. They are going to do a "good will repair" on my bike, so I imagine it's the same for anyone with a 1300.
When I'm back in the U.S. getting my bike repaired I thought I might look into upgrading my pipes as well. Has any one put Hard Kromes on their bike?