transmission question

[hogmandon]

I have an 06 RG that I put the SE 6speed in. All was good for maybe 10 t0 12,000 m and it then got noisy in 4th and 6th gear. It got to the point I couldn't stand it so I picked up and installed the Baker rebuild kit. I really like the ratios and the way it shifts but now 14,000m later it is noisy again so much I am afraid to go far with it. All the gears are quiet except 4th and 6th. Can anyone tell me what is the weak bearing or part that is making the noise in these gear sets. I heard about the complaints of noise but never thought they were going to be so loud. I think 5th gear power goes in and out the same shaft 4th and 6th power comes in the main shaft from the clutch then out the front shaft via gears and back to the main shaft final pulley. The only differences I see is the pressed in roller bearing on the front shaft. When I did the rebuild, that roller bearing looked fine but replaced it any way. Any info and help would be greatly appreciated.

[SmokyOwl]

Are you doing anything unusual in those gears?  Maybe your riding style/area is harsh on those gears and you bend the shift forks?  Just spitballing.  Multiple transmissions with the same problem, at similar mileages, makes me think something consistent and otherwise benign is happening over the course of 10,000 miles.
I have an '06 with the se 6-speed, only problem I've had since day one is the frequent stuck halfway sixth gear and I have to hit the shifter twice sometimes to get it fully engaged.  I think I'm somewhere about 20-25k miles on it now but haven't had any noise issues from it at all.