I must admit I too am a little concerned about pump vibration. I've seen other builds where the pump is attached to the side or top of the HDD caddy so I'm hoping its not too bad. The mounting feet are rubber and very flexible and also I've left a gap around the body, when I cut the big hole, so that it doesn't touch.
Otherwise I'll have to get busy with the foam as you suggest. Or break out the Meccano!