Just to update. I have done a few things that have improved 3rd gear noise a little.
1/ 10W50 fully synthetic engine oil
2/ I applied 10mm self adhesive sound proofing foam to the top of the oil tank, to the underside of the fuel tank (Not above the air box) and to the inside of the little side panels under the front of the seat.
3/ I have Dynojetted the carbs (with the open pipe and pipercross filter that were already fitted)
Now, don't get me wrong, this has not done away with the noisy 3rd gear altogether. But I'm sure it's better. In fact, unless I'm imagining it, it seems to be getting better a little each time I ride it. I think the biggest improvement is the Dynojet kit. It makes the engine much smoother at low revs which seems to stop 3rd gear chattering quite so much on light throttle. And also, even though I run 17/42 gearing, it'll pull 4th gear at 30mph now, which it wouldn't do nicely before,meaning I spend less time in 3rd. The only down side is I'm down to about 45mpg, but I have more performance so...
I guess what I should add is, I have for the last decade or so worn ear plugs. And for this summer I bought my self a Sena intercom thingy, brilliant thing! I can listen to the radio from my phone with it as well as make calls and the like. But I don't always wear it, it depends on how far I'm going.
Also, my clutch is running the later stiffer Yamaha clutch springs and Wemoto steel (oil dimpled) clutch plates. I guess the thicker oil might make the clutch slip if it had the lighter clutch springs fitted.