2004 - 24500 miles, full dealer history.. No problems with bumps, just clutch..
then you can rasonably assume it's not the mounts, etc. If I had to wager a guess, given the year of the car, I would think a faulty throw out bearing. Quite common. While in there, check the obvious things such as clutch disk condition, pressure plate fingers (to make sure they are all even and one/some have not collapsed) as well as torque on the flywheel bolts
unlikely to be the mounts as these are usually noticable on deceleration aswell as acceleration, but i dont understand why the clutch would only cause a prob in 1st and 2nd ? unless its driving more and momentum helps in the higher gears
very difficult to diagnose a noise via the net though