Here is my take on this project. I have updated the protype board to stacked PC Arduino boards. In addition I made PC boards for the LED to mount to underneath the display top. I also mirrored the case on the bottom and the back of the cube enclosure. All of the LED leads attached to the stacked boards by ribbon jumper cables. all control switches and and status lights will be located on the sloped front panel. the USB programing port, power switch, and power cord will be located in the back. Just have the power supply, and the PC boards to finish and install.
OK, Here I hope this helps you out, here is a better look at the boards and a list of the chips on them.
MAX232CPE Multichannel RS-232 Drivers/Receivers
ATMEGA32A CPU 8-bit Micro-controller with 32K Bytes In-System Programmable Flash
the top board connects to the bottom via a 16 pin and a 2 pin connector.
8 74HC574N Octal D-type flip-flop; positive edge-trigger; 3-state
74HC138N 3-to-8 line decoder/demultiplexer; inverting
I am currently working on the PC board that the led's will solder to underneath. It will have 8 pin connectors for easy connection to the main board. it's the last photo. I will up date this as soon as the boards are made.