Sorry, I do not have full writeup for this project. Here is a photostream of the mod.
Pretty much what I did was take an off the shelf strobe light and swap it for the one built into the fog machine. Re-wired a ps/2 keyboard cable connecting it to the liberated rock band strobe light. Now I can use the strobe light with the game without dragging out the fog machine.
Also added override switches on the fog machine so I could activate both the strobe and fog machine outside the game.