I found a low cost, easy way to fabricate an electronics stack cover for your ArduCopter. You will need:
1 Ziploc Brand Container, Medium Square size
4 Rubber Bands, 1"-1.5" diameter
Modify the container by cutting 8 "posts" in the lip for fastening the rubber bands. See my closeup:
Then simply fasten the container over your stack by running the rubber bands from one binding post, under the quad arm, and then up to the binding post on the other side of the arm, like so:
Here is a picture of the completed copter. (The two black dots at the top are my arming and GPS status LEDs).