Midi sync for cdj-800

  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?