Ok... for being a novice just trying to get my bearings, I still find the code a bit confusing, even though you comment well. I'll get there. I hoped there would be more straight forward coding using decimal or hex, without having too many variables. I forgot to mention that my Arduino is flashed with HIDUINO, and I am programming the 2560 via ISP.
Here are some screen shots showing the exact MIDI messages that are being sent and received between my audio recording program and my external controllers:
Here, the "incoming" messages are in HEX, these are the messages being sent from my audio recording program. Bome's MIDI translates that message and shows the "outgoing" code to the external controller, which is what it wants to see to function properly.
This image shows "incoming" messages from the controller, and Bome's MIDI translates that message and shows the "outgoing" code to the audio recording program, which is what it wants to see to function properly.

Here is the code I've started for that PING I mentioned earlier, which is "pinging" properly, but also my attempt at sending this data the way I thought it needed to be sent. Comments are welcome:
#include <MIDI.h>
#include <stdlib.h>
#include "Arduino.h"
#include "HardwareSerial.h"
#define LED 13
MIDI_CREATE_DEFAULT_INSTANCE();
// -----------------------------------------------------------------------------
//This sketch programs the MEGA2560 to receive a HUI ping and return that ping
//back to HUI to allow external controller conversion to occur. Arduino is bootloaded
//with HIDUINO firmware on the Atmel8u2 as a class-compliant driverless MIDI device,
//passing MIDI messages through it. Programmed via ISP as the HIDUINO firmware does not
//allow for USB<>Arduino sketch programming.
void Ping(byte channel, byte pitch, byte velocity)//channel 1, pitch 0, velocity 0
{
if (velocity==0);
digitalWrite(LED, LOW);
delay(400); //LED flash for 1/2 second to confirm Ping Return
digitalWrite(LED, HIGH);
MIDI.sendNoteOn(0, 127, 1);//note, velocity, channel
delay(5);
MIDI.sendNoteOff(0, 127, 1);
// Notice that NoteOn messages with 0 velocity are interpreted as NoteOffs.
}
void Channel_1(byte channel, byte pitch, byte velocity){
//Mute Press On Track Channel 1 from Pro Tools to Controller
if(channel==176, pitch==12, velocity==0, channel==176, pitch==44, velocity==2);
byte Mute_1[] = {176,70,127,176,70,0};
Serial1.write(Mute_1,6);
delay(50);
if(channel==176, pitch==12, velocity==0, channel==176, pitch==44, velocity==66);
byte Mute_1_1[] = {176,70,127};
Serial1.write(Mute_1_1,3);
}
// -----------------------------------------------------------------------------
void setup()
{
Serial1.begin(38400);//Serial 1 pin 19(Rx) pin 18(Tx)
MIDI.setHandleNoteOff(Ping);
MIDI.setHandleNoteOn(Channel_1);
// Initiate MIDI communications, listen to all channels
MIDI.begin(MIDI_CHANNEL_OMNI);
}
void loop()
{
// Call MIDI.read the fastest you can for real-time performance.
MIDI.read();
}