Encoder code using interrupts design question

Question

I have an Arduino Mega 2560, an Omron Optical encoder with an Index (360 steps), a 60 led NeoPixel ring (no Clk wire) and another Arduino Uno. Here is my question, I have some code written that works with the Arduino Mega and optical encoder outputting decently to the serial monitor for diagnostic purposes. When I add the additional code to run the Neopixel ring I get a terrible response on the ring. I have tried the NeoPixel and FastLED libraries with the same terrible success. It even states in their documentation that they don't work well with interrupts. I started thinking about sending the 3 digit output to a Direct Pin output from the Mega to be read by another Mega/Uno to run the Neopixel Ring and a 4x20 LCD screen. Does anyone else have any ideas on this. Below is my code for the Mega and the Encoder.

    // Wiring connections for my encoder:
    // Brown : VCC = 5V
    // Blue + Shield : 0V = GND
    // Black : ENCODER0PINA, Pin 18
    // White : ENCODER0PINB, Pin 17
    // Orange : ENCODER0PINI, Pin 19

    #define ENCODER0PINA         18      // this pin needs to support interrupts
    #define ENCODER0PINB         17      // no interrupt required
    #define ENCODER0PINI         19      // this pin needs to support interrupts

    // variables modified by interrupt handler must be declared as volatile
    volatile long encoder0Position = 0;
    volatile long interruptsReceived = 0;
    volatile byte INTFLAG1 = 0;

    // track last position so we know whether it's worth printing new output
    long previousPosition = 0;

    void setup()
    {
      // inputs
      pinMode(ENCODER0PINA, INPUT);
      digitalWrite(ENCODER0PINA, HIGH);  // turn on pullup resistor
      pinMode(ENCODER0PINB, INPUT);
      digitalWrite(ENCODER0PINB, HIGH);  // turn on pullup resistor
      pinMode(ENCODER0PINI, INPUT);
      digitalWrite(ENCODER0PINI, HIGH);  // turn on pullup resistor

      // interrupts
      attachInterrupt(5, onInterrupt, RISING);  // encoder track A on interrupt 3 - pin 18
      attachInterrupt(4, onReset, RISING);  // encoder Index track on interrupt 4 - pin 19

      // enable diagnostic output
      Serial.begin (115200);
      Serial.println("Ready.");
    }

    void loop()
    {
      // only display position info if has changed
      if (encoder0Position != previousPosition )
      {
        Serial.println(encoder0Position, DEC);

        previousPosition = encoder0Position;
      }
    }

// interrupt function needs to do as little as possible

void onInterrupt()
{
  // read both directional inputs
  int a = digitalRead(ENCODER0PINA);
  int b = digitalRead(ENCODER0PINB);

  if (a == b)
  {
    // b is leading a (counter-clockwise)
    encoder0Position--;
    if (encoder0Position < 0)
    {
      encoder0Position = ((encoder0Position + 360) % 360);
    }
  }
  else
  {
    // a is leading b (clockwise)
    encoder0Position++;
    if (encoder0Position >= 360)
    {
      encoder0Position = ((encoder0Position - 360) % 360);
    }
  }
}

void onReset()
{
  // read Index input
  int i = digitalRead(ENCODER0PINI);
  if (i == 1)
    {
  encoder0Position = INTFLAG1;
    }
}