May 2011 build, my car makes the exact same noises. I think it's the clutch - maybe synchros? Just over 33k miles here.
I feel like it makes a weird noise in reverse too, but I could be crazy. Anyway, I have these same noises (just as bad, occasionally worse) going from 1->2, 2->3 and sometimes more. My car hasn't shifted as smooth as the video VectorZ posted in a while... I'll take a video with RPM on the way home for you guys. You'll notice my RPMs spike right before the upshift...
EDIT: Aside from the weird lurching and grinding, she does still drive.