I am not mechanic, but it sort of sounds like the flywheel. Have you ever ground the gears badly? It is odd that only 1st and 2nd are harsh, and not all the gears. Also, once you've shifted does the sound stop, or is it there the entire time your in 1st and 2nd gear?
It could also be that you aren't pushing the clutch in all the way, try putting your seat all the way forward and pressing the clutch down entirely. It sounds stupid, but sometimes it is just something simple.
Merry Christmas!
