Regarding the lights/outputs I've decided to create a separate output board using daisy chained shift registers. This output board will be connected to the lights- and display-microcontroller. The beauty about this thing is that it costs almost nothing and once the values are set, they are there until you reset them.
More or less - I simply send all my data to a specific output-pin and the shift registers push/pop values throughout the registerchain. In theory I could chain a lot of them together, but for now I've decided to settle for 8 chips in a row using the 8bit 74HC595. If it all works out as intended I will add additional chips. This combined with the 54 I/O's on the Arduino Mega 2560 should be plenty!
By the way, my Sparkfun backorder on the Arduino board (damn those things sell out fast!) has arrived, so they should be shipping it soon... Then we can get this party started!