Another "also": Over the last few days I was reading this thread and giving it some thought. I was intrigued by your description, that it was noticeable in one gear and not in others.
The only thing I could come up with was this: In a standard 6 speed Constant-Mesh motorcycle gearbox you have two shafts, the "drive" and the "driven". This entire assembly turns (is carried by) four bearings, one at the end of each shaft. You would think that if one of those bearings was going to make noise it would do it no matter what gear ratio I engaged.
But while thinking about your problem I began to wonder if that's not true because when you select different gears the vector of force within the gearbox changes. There are some good demonstration videos of motorcycle gearboxes that are posted up on YouTube that you can watch to see this. With every gear change the path of power transfer through the gearbox also changes. Each of these unique pathways has its own unique vector of force and that vector will affect the four bearings that support the gearbox differently.
This might explain your experience with the sound/vibration/thrumming feeling.