Looking at that Typhon controller and what you want to do with it, Cornelius, I'm wondering why you want to use that controller. Since you're going to be re-writing it I don't see much advantage in using it; you could get the same functionality with a regular Arduino controller and a display shield -- or just get a separate display and a few switches and build your interface (would make for a simpler enclosure...).
I assume that due to the display and switches that the Typhon is cramped to just 4 PWM outputs for LED drivers. A typical Uno-compatible will have 6 PWM outputs or you could get a Mega with 14 (and save money by only needing one board).