Help to modify the Gijs's master clock generator.

Hi there,
first of all, I have to tell you that I am not very comfortable with programming. I am still learning.
Here is my problem.
I have made the Gijs's MCG without any problem. It works well. But now I would like to modify it to be able to control an akai headrush E1.

The first mod I'd like to make:
I have done several attempts to add a second LED which would blink in time with the midi/sync24/... clocks.
Every test I made wasn't accurate att all and the tempo LED (the one already there) changed his blinking frequency as I started the second LED. I tried with delay() but of course it delays other things, with millis() but I lost myself in calculation as I need a short LOW and long HIGH blinking (or the opposite)

I someone could help me with this, that would be great.

At the end the project would be something like that:

-plug the two switches of the headrush in the arduino (to tell the arduino what the headrush is doing and to control the headrush) since the two switches are dpdt footswitches with only one side used by the headrush.

-write a code for the arduino to send a start/stop message to the headrush in time with the other gear connected and acting differently if the REC button of the headrush is ON or OFF.

I am sure this is not so hard but I am bad enough not to know from where I can start all this.

here is the MCG I am using:

/*
--------------------------------------------------------------------------------------------------
Master Clock Generator V0_1 (januari 2008):
MIDI, LSDj, nanoloop and sync24 PITCH CONTROLE/CLOCK GENERATOR with Start/Stop for MIDI and sync24
By: Gijs Gieskes 2007/2008

MIDI Clock out on Pins: 8 and 9.
LSDj Clock out on Pins: 10 to 13. 
sync24 start/stop out on Pin: 2 and 3.
sync24 on analog Pins: a1 and a2
nanoloop/sync12 on analog Pins: a3 to a5
LED Start/Stop indication on Pin: 4.
LED Clock indication on Pin: 5.
Stop Button on Pin: 6.
Start Button on Pin: 7.
potentiometer on Pin: a0
--------------------------------------------------------------------------------------------------
*/

int analogValueA = 0;
int SSdin1 = 2;
int SSdin2 = 3;
int ledOnOff = 4;
int ledPin = 5;
int SSButton2 = 6;  
int SSButton1 = 7;   
int SSRead1 = 0;
int SSRead2 = 0;
int eenKeer = 1;          
int ledTeller = 0;
int nanoOnOff = 0;

void setup(){
  DDRB = B111111;  
  DDRC = B111100;             
  pinMode(SSdin1, OUTPUT);   
  pinMode(SSdin2, OUTPUT);      
  pinMode(ledPin, OUTPUT);       
  pinMode(ledOnOff, OUTPUT);     
  pinMode(SSButton1, INPUT);     
  pinMode(SSButton2, INPUT);   
  digitalWrite(ledOnOff, LOW);    
  digitalWrite(SSdin1, LOW);       
  digitalWrite(SSButton1, HIGH);      
  digitalWrite(SSButton2, HIGH);      
}

void loop(){
  
  analogValueA = analogRead(0);
  analogValueA = 2200+(analogValueA*10);  // delay settings
  
  SSRead1 = digitalRead(SSButton1); 
  SSRead2 = digitalRead(SSButton2); 
  
  if (SSRead1 == LOW && eenKeer == 1) { 
    eenKeer = 0;
    Cstart();
    lsdjClock(eenKeer); 
    digitalWrite(SSdin1, HIGH); 
    digitalWrite(SSdin2, HIGH);
    digitalWrite(ledOnOff, HIGH); 
    nanoOnOff = ClockDelay(analogValueA, nanoOnOff, eenKeer);
  }
  
  if (SSRead2 == LOW && eenKeer == 0) { 
    eenKeer = 1;
    Cstop();
    digitalWrite(SSdin1, LOW); 
    digitalWrite(SSdin2, LOW); 
    digitalWrite(ledOnOff, LOW);
    nanoOnOff = ClockDelay(analogValueA, 1, 1);
  }
  
  midiClock();
  lsdjClock(eenKeer);
  ledTeller = ledCounter(ledTeller);
  nanoOnOff = ClockDelay(analogValueA, nanoOnOff, eenKeer);
  
}

void midiClock(){
  PORTB = B111100; 
  delayMicroseconds(128); 
  PORTB = B111111;
}

void Cstart(){
  PORTB = B111100;    
  delayMicroseconds(64); 
  PORTB = B111111;  
  delayMicroseconds(32);
  PORTB = B111100; 
  delayMicroseconds(32);  
  PORTB = B111111;
}

void Cstop(){
  PORTB = B111100;
  delayMicroseconds(96);
  PORTB = B111111;
}

void lsdjClock(int eenKeer){
  if(eenKeer == 0){
    for (int i=0; i <= 7; i++){
      PORTB = B000011;
      delayMicroseconds(61);   
      PORTB = B111111;
      delayMicroseconds(61);  
    }
  }else{
    delayMicroseconds(976); 
  }
}
 
int ClockDelay(int clockspeedA, int input, int eenKeerIn){
 if(input == 1){
   if(eenKeerIn == 1){
     PORTC = B111110;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
     PORTC = B111000;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
   }else{
     PORTC = B111110;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
     PORTC = B111000;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
   }
   return 0;
 }else{
   if(eenKeerIn == 1){
     PORTC = B111110;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
     PORTC = B111000;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
   }else{
     PORTC = B000110;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
     PORTC = B000000;
     delayMicroseconds(clockspeedA);
     delayMicroseconds(clockspeedA);
   }
   return 1;
 }
}

int ledCounter(int input){
  if(input < 23){
    if(input < 12){
      digitalWrite(ledPin, HIGH);
    }else{
      digitalWrite(ledPin, LOW);
    }
    return input+1;
  }else{
    return 0;
  }
}

I have also tried this one but that worked until I tried to make the HIGH longer than the LOW.
I am still learning and testing with some tutos found on internet but as soon as I think I have found, something is blocking me.
For example how to adapt the code into the MCG code.
How can I sync the MCG clock to my led blinking.
etc etc...
But don't worry I am still triyng everything around.

any help still welcome though