pinMode(lengthLEDPin, OUTPUT); // mode Iidicator
pinMode(dutyCycleLEDPin, OUTPUT); // mode indicator
pinMode(stutterLEDPin, OUTPUT); // mode indicator
pinMode(alignLEDPin, OUTPUT); // mode indicator
pinMode(12, OUTPUT); // Cue button presser
pinMode(13, INPUT); // activate button
pinMode(14, INPUT);
pinMode(15, INPUT);
pinMode(16, INPUT);
pinMode(17, INPUT);
Oh I see. Why did you stop using symbolic names from pins 12 onwards? Get bored?
How about:
pinMode(alignSwitch, INPUT);
pinMode(lengthSwitch, INPUT);
pinMode(stutterSwitch, INPUT);
pinMode(dutycycleSwitch, INPUT);
And so on for the rest of the sketch. Although judging by this bit, I guessed the names wrongly:
alignMode = digitalRead(17);
stutterMode = digitalRead(16);
dutyCycleMode = digitalRead(15);
lengthMode = digitalRead(14);
activate = digitalRead(13);
Good use of symbolic names makes it easy to read. Easy to read is easy to debug.
How are the switches wired up exactly? Are there pull-up or pull-down resistors?