I've been trying to pinpoint what exactly causes the vibration to come back, and I think I have an idea. Usually it's after a WOT pull to near-redline, regardless of if it's in 4th gear on the highway or in 2nd on the street.
What I have noticed though is that if I am about to shift up with the pedal to the floor, and make a conscious effort to lift my foot off the gas just a fraction of a second earlier (so that the gas is no longer being pushed at all by the time the clutch is all the way in, i.e. no revs jumping up further, even slightly, when the clutch is pushed in), the vibration doesn't happen. However, if I shift even slightly sloppily (push the clutch in and the revs jump up slightly due to not having my foot fully off the gas yet), the vibration comes back almost 100% of the time.
Still testing this theory, so let me know if you guys find the same or not. Of course, still no idea at all as to what the mechanical cause could be. But it least it seems like if you make upshifts precise and don't get lazy shifting, leaving your foot on the gas, this prevents the vibration from occuring. Could be wrong.