2005 R1 Gearbox diagnostics

I have a 2005 R1 and need some help where to start looking/considering what the problem might be given the following:

1. Start the bike it runs quiet and smooth as expected.

2. After the bike has warmed up for about 5 minutes, an audible 'rotating' sound(sorry I do know how else to articulate it) is heard from where the gearbox is. I can hear it on the countershaft sprocket side and on the clutch cover side, i.e. both sides.

3. The longer the bike is run, the louder the 'rotating' sound is. To the point you can hear it with a helmet on.

4. Anyone know what this might be? Where to start looking? I took the countershaft sprocket cover off and everything is ok with that. It is internal.

5. Has anyone else heard of these problems with this bike?

6. The bike has about 4000 miles on it.

thanks,

Kevin