jQuery Create variable name from each value in array

Update on updated fiddle

It seems I got what you are trying to do and what you problem is. There is two lines of code in your updated fiddle

    ATMCXPDate[index] = [$(this).find(":nth-child(1)").html()]; //set dates found in column into array and assign variable name

    ATMCXPTime[index] = [minutes]; //set converted minutes from column into array and assign variable name

which is either typo or you forget to declare index variable. As you want to have one array for all dates and another for all times from all tables that you have , you are to replace it with

   ATMCXPDate.push($(this).find(":nth-child(1)").html());
   ATMCXPTime.push(minutes); 

We are doing 2 things here, putting just parsed date and time into arrays and putting just plain values , not wrapped up into arrays as you had it before, you don't need array inside array.

Update on performance of original code:
There are several things that seems to be logical errors

• You have extra cycle for ( i in Sys)
• You can select table once and iterate through rows after that ( $('#' + CritPath[i] + ' tbody tr') replaced with $('#'+CritPath[i]).find('tr').each

One obvious error with your code is that you are creating variables with the same name both in global scope and in the function. ie

...
// here you created global variables and assigned them to empty arrays
var SysDate = [];
var SysTime = [];

$(function(Sys){
    for (i in CritPath) {

        // here you created local variables with the same names so global ones are no more accessible within this function
        var SysDate = Sys+'Date';
        var SysTime = Sys+'Time';

    for (i in Sys) {
        $('#' + CritPath[i] + ' tbody tr').each(function(index) {
            ...
            // here you assigned local variables , but
            SysDate[index] = [$(this).find(":nth-child(1)").html()];

            // this line doesnt make sense
            SysTime[index] = [index] = [minutes];
            // you probably meant 
            SysTime[index] = [minutes];
        });
    }
   }
// next line just doesn't make any sense as it is not used anywhere
return Sys;
});
// here you alerting global variables, that wasn't affected by your ondomready    handler
alert(SysTime);
alert(CritPath);
alert(Sys);

Overall if you want to create variable in the global scope with particular name you can do this using window object

function setVar () {
  var nameOfGlobalVariable = 'SysTime0202'
  window[nameOfGlobalVariable] = 'some value'
}

setVar()

console.log(SysTime0202)  // outputs 'some value'

I suspect that you really don't need global variables with different names and instead you need just pair of array for both dates and times you have. I expect that you want to do a lookup by one date / time and get corresponding value from another array , just different critical path from you set of critical paths.

You can try do to something like

var CriticalPathData = []
$(function(){ 

  // looping through named tables to grab all date/times
  for (var i in CritPath) {

    var cp = CritPath[i]
      , table = $('#' + cp)
      // this is object which will hold all date/times for particular critical path
      , cpDateTime = { items : [] }


        table.find('tr').each(function(index, row) {
            var $this = $(this)
              , tds = $this.find('td')
              , rowDate = tds[0].innerHTML
              , rowTime = tds[1].innerHTML
              , parsedTime = rowTime.split(':')
            cpDateTime.items.push({ Date: rowDate , Time : +parsedTime[0] * 60 + +parsedTime[1] })  
        });
      // put parsed dates/times for all items with critical path to global object
      CriticalPathData.push(cpDateTime)
   }

   // after you filled in all the data you can access it here
   alert(CriticalPathData[0].items[0].Date)
   alert(CriticalPathData[0].items[0].Time)
})   

// or here
alert(CriticalPathData[0].items[0].Date)
alert(CriticalPathData[0].items[0].Time)