I have had some setbacks. :( I used solid wire for connecting the LEDs and movement around them resulted in breakage of the leads off a couple LEDs. The LEDs are glued pretty solidly into the acrylic box. Back to the drawing board! (And a replacement box ordered.)
I'm rethinking the wiring to the LEDs. I need to use stranded wire and fasten the wire near the LEDs to reduce movement. Second, I plan to use headers on the interconnect board and socketed leads on the LEDs rather than solder everything. That way I can get the interconnect board in place and then easily make all of the connections. (The interconnect board holds the series resistors for the LEDs, the grounding resistors for the push buttons and a small amp for the speaker.) As I pondered that, I realized that I could put the processor on the interconnect board as well, eliminating all of the connections between the Arduino I/O sockets and the interconnect board. Except for the lack of an Arduino for my son to play with, this will make a much cleaner project. But it also opens up a couple more issues I need to investigate.
Can I apply S/W updates in circuit using another Arduino (Quick research - yes: http://arduino.cc/en/Tutorial/ArduinoToBreadboard.)
Does power via a USB connector require conditioning or regulation? I looked at the circuit diagram and could not answer that. I see the 5V pin from USB going through a pot and I don't see where it goes from there. At a minimum it seems like a bypass cap would be wise.
I plan to socket the ATMega chip. It might make it easier to reprogram (though the connections in the tutorial I cited above look pretty straight forward.) It also makes it easy to test out the peripherals by connecting I/O pins from an Arduino Uno (or breadboarded chip) to the corresponding pins in the socket.
But back to the LEDs. I also plan to put a dab of silicone sealer at the base of the LEDs to act as a bit of a strain relief (along with a bit of shrink wrap over the solder connection. And finally... A dab of silicone sealer to hold the LEDs in their holes rather than super glue. If I need to remove them for some reason,it should be possible.