Took the car in to my local dealer and took a ride w/ one of their techs on the highway. He definitely felt the problem as in my car it occurred 90% of the time when shifting at around 5-6k.
They opened everything up, and their diagnosis was "Clutch throw out bearing loose and grinding causing premature wear to clutch." They replaced the flywheel, clutch, pressure plate, spring release lever retainer, and throwout bearing (and a couple misc gaskets bolts and spring on the exhaust assembly), all under warranty.
Got the car back and the first thing I noticed was the clutch pedal felt light as a feather compared to earlier! Car drives great now, and no more issues with vibration so far!
Props to Cityside Subaru in Belmont, MA. The guy working on my car (think his name was Brian) was pretty cool.