These units look great! I built a similar thing with 2x2 units but using sparkfun's serial matrix... (http://www.youtube.com/watch?v=Q7BnNd866O8)
I found that project from a post on the Sparkfun website, and it is awesome! Any chance you might write up how you built it and/or maybe share the code? I would love to try and build on like yours. The only 'flaw' with the RainbowDuino is the fact that it does not allow a 2x2 matrix like you made.