//Define column and limit for each
var checkboxConfig = [
    {name: col1, limit: 3},
    {name: col2, limit: 3},
    {name: col3, limit: 3},
    {name: col4, limit: 3}
];
 
 
//Set variable for array as a whole
for (i = 0; i < checkboxConfig.length; i += 1) {
setLimit(checkboxConfig[i].name, checkboxConfig[i].limit);
}
 
//Assign Click Handler for each checkbox
function setLimit(name, limit) {
  var els = document.getElementsByName(name); 
  for (i = 0; i<els.length; i += 1) {
    els[i].onclick = checkboxClickHandler(els[i], limit);
}
}
//New function for each click handler
function checkboxClickHandler(el, limit) {
    return function () {
        limit_checkbox(el, limit);
    }
}
 
//Limit checkbox function 
function limit_checkbox(el, max) {
    var count = 0,
        i;
    var checkboxes = document.getElementsByName(el.name);
    for (i = 0; i < checkboxes.length; i += 1) {
        if (checkboxes[i].checked) {
            count = count + 1;
    }
  }   
    if (count > max) {
alert('Please select only ' + max + ' checkboxes.\
To select this option unselect one of the others.');
        el.checked = false;
    }
}

<script type="text/javascript" charset="utf-8">
$(document).ready(function() {
  limit_checkbox(‘{el}’,[‘col1’,’ col2’,’ col3’,’ col4’])
});
 
  var col1 =  {688526X267X7389SQ001_SQ001,688526X267X7389SQ002_SQ001,688526X267X7389SQ003_SQ001,688526X267X7389SQ004_SQ001};
  var col2 =  {688526X267X7389SQ001_SQ002,688526X267X7389SQ002_SQ002,688526X267X7389SQ003_SQ002,688526X267X7389SQ004_SQ002};
var col3 = {688526X267X7389SQ001_SQ003,688526X267X7389SQ002_SQ003,688526X267X7389SQ003_SQ003,688526X267X7389SQ004_SQ003};
  var col4 = {688526X267X7389SQ001_SQ004,688526X267X7389SQ002_SQ004,688526X267X7389SQ003_SQ004,688526X267X7389SQ004_SQ004}; </script>

<script type="text/javascript" charset="utf-8">
  $(document).ready(function() {
 
    // Define the maximum answers per column
    var maxAnswers = 3;
 
    // Identify this question
    var thisQuestion = $('#question{QID}');
 
    // Index the array columns
    $('table.subquestion-list tr', thisQuestion).each(function(i) {
      $('> *', this).each(function(i) {
        $(this).attr('data-index', i);
      });
    });
 
    // Listener on the checkboxes
    $('input[type="checkbox"]', thisQuestion).on('change', function(e) {
      var thisIndex = $(this).closest('.answer-item').attr('data-index');
      $('[data-index="'+thisIndex+'"] input[type="checkbox"]', thisQuestion).prop('disabled', false);
 
      // If max reached, disable unchecked inputs in this column
      if($('[data-index="'+thisIndex+'"] input[type="checkbox"]:checked', thisQuestion).length >= maxAnswers) {
        $('[data-index="'+thisIndex+'"] input[type="checkbox"]:not(:checked)', thisQuestion).prop('disabled', true);
      }
    });
  });
</script>

<script type="text/javascript" charset="utf-8">  
  $(document).ready(function() {
 
    // The answer code to place in the last position
    var fixedCode = 'SQ004';
 
    // Identify this question
    var q1ID = {QID};
    var thisQuestion = $('#question'+q1ID);
 
    // Move the "fixed" row to the end
    $('multiflexible_checkbox', thisQuestion).append($('div[id^="javatbd"][id$="X'+q1ID+fixedCode+'"]', thisQuestion));
 
    });
</script>

<script type="text/javascript" charset="utf-8">
  $(document).ready(function() {
 
    // Define the maximum answers per column
    var maxAnswers = 3;
 
    // Identify this question
    var thisQuestion = $('#question{QID}');
 
    // Index the array columns
    $('table.subquestion-list tr', thisQuestion).each(function(i) {
      $('> *', this).each(function(i) {
        $(this).attr('data-index', i);
      });
    });
 
    // Listener on the checkboxes
    $('input[type="checkbox"]', thisQuestion).on('change', function(e) {
      var thisIndex = $(this).closest('.answer-item').attr('data-index');
      $('[data-index="'+thisIndex+'"] input[type="checkbox"]', thisQuestion).prop('disabled', false);
 
      // If max reached, disable unchecked inputs in this column
      if($('[data-index="'+thisIndex+'"] input[type="checkbox"]:checked', thisQuestion).length >= maxAnswers) {
        $('[data-index="'+thisIndex+'"] input[type="checkbox"]:not(:checked)', thisQuestion).prop('disabled', true);
      }
    });
 
    // The sub-question code to place in the last position
    var fixedCode = 'Y004';
 
    // Move the "fixed" row to the end
    $('table.subquestion-list tbody:eq(0), table.subquestions-list tbody:eq(0)', thisQuestion).append($('tr[id$="X'+{QID}+fixedCode +'"]'));
 
    // Fix up the row background colours
    $('table.subquestion-list tbody tr, table.subquestions-list tbody tr', thisQuestion).each(function(i){
      $(this).removeClass('array1, array2');
      if(i % 2 == 0) {
        $(this).addClass('array1');
      }
      else {
        $(this).addClass('array2');
      }
    });
  });
</script>