Tough call...
You've done your homework, that's for sure. I agree...normally crank or rod bearing will get louder...and they won't be loud very long, just a bang and dead stop.
Question...does it go away if you pull your clutch lever in?
Maybe something is loose in the actuator arm, which...is by the left side of the motor.
Since you took it apart and it looked good...this is a tough one. I really hate to say it, but...it might be time for a tear down and measurement on everything.
Or...you could just ride it that way, wait till it (If it does) gernades...and rebuild it from the ground up. That's the non-preferred expensive way, however...
On a side note, once you get this sorted...set the plate back to 0 and use the third setting on the Dyna...and get some 110 octane to be safe if you can.
My Dyna gets here Friday, I can't wait to hook it up to my laptop to mess with the curves!!
Sorry i'm not much help on this one...hope you get it figured out.