Try this, get the revs in 1st almost to the red line and then put the clutch in and leave it in first gear. Listen for noise, it may actually get a bit louder once you're moving a bit slower.

If you hear noise, move the shifter out of 1st and see if it goes away.

You can do the same with 2nd, unlikely you'll be able to hear anything in the taller gears.

If you hear something while doing that you know what you're hearing is a trans. bearing(s) issue, although not necessarily related to what you're asking about.
If you heard nothing while doing this (make sure it's as quiet as possible) than you know to look elsewhere than the trans. itself.

I've got a bit of noise on my car when I do that but not when taking off like you describe. I've found using synthetic 10w30 (as opposed to dino 10w30) has quieted it down a bit, though it took a while. Soon Honda MTF will be in there.