Sorry mate - don't have the time to go through this in detail but here are
some pointers:
General
* When referring to a sheet it helps to be specific - define a sheet
variable and use it - using activesheet is too ambiguous
* There is a lot of selecting going on - when you are doing stuff in excel
vba you rarely need to select it - the selection is just a range - it is much
easier to be specific about the range which you want to work on
* Likewise - activecell - what may ar may not be active is sometimes unclear
- be specific about the cell you want to work on
Specific
* As you say, the macro assumes 2 sheets of data
* You need to modify it so you create a loop to determine how many sheets
you have created and then just work on those sheets
* Probably be better to have sheets with raw data in it and then create
sheets (maywe in another book) where you copy the unique items to - that way
you have a complete trail of data)
* create a criteria sheet for your criterias (seem to be hiding them at the
bottom of the worksheet)
Hope this helps

Try these changes.  It is not fully tested, but it should help.  I wasn't
sure which worksheets were being deleted so I didn't put these statement in
the code below.

Sub FileImport()

     'Dimension Variables
     
     Dim ResultStr As String
     Dim FileName As String
     Dim FileNum As Integer
     Dim Counter As Double
     Dim MySheets(1) As Worksheet
     Dim NumberSheets As Integer
     
     'Filename for Txt file
     FileName = "\\Hdqfs001\public_hdq014-fs02\" & _
        "Revenue Accounts\REVERA\Systems_analysis\" & _
        "JD_month_end_reports\Trans volumes per card type.txt"
     
     'Get Next Available File Handle Number
     FileNum = FreeFile()
     
     'Open Text File For Input
     Open FileName For Input As #FileNum
     
     'Turn Screen Updating Off
     Application.ScreenUpdating = False
     
     'Create A New Worksheet
     ActiveWorkbook.Sheets.Add
     Set MySheets(0) = ActiveSheet
     NumberSheets = 1
     'Set The Counter to 1
     Counter = 1
     
     'Loop Until the End Of File Is Reached
     Do While Seek(FileNum) <= LOF(FileNum)
     
        'Display Importing Row Number On Status Bar
         Application.StatusBar = "Importing Row " & _
            Counter & " of text file " & FileName
           
         'Store One Line Of Text From File To Variable
         Line Input #FileNum, ResultStr
         
         'Store Variable Data Into Active Cell
         If Left(ResultStr, 1) = "=" Then
            ActiveCell.Value = "'" & ResultStr
         Else
            ActiveCell.Value = ResultStr
         End If
         
         'If on the last row of worksheet create a new worksheet
         If ActiveCell.Row = 65536 Then
            ActiveWorkbook.Sheets.Add
            NumberSheets = NumberSheets + 1
            ReDim Preserve MySheets(NumberSheets)
            MySheets(NumberSheets - 1) = ActiveSheet
         Else
            'If Not The Last Row Then Go One Cell Down
            ActiveCell.Offset(1, 0).Select
         End If
         
         'Increment the Counter By 1
         Counter = Counter + 1
     
     'Start Again At Top Of 'Do While' Statement
     Loop
     
     'Close The Open Text File
     Close
     
     'Remove Message From Status Bar
     Application.StatusBar = False
     
   With MySheets(0)
      'Select the first column of the first worksheet created
      .Range("A1").Select
      .Range(Selection, Selection.End(xlDown)).Select
   
      'Convert the imported text rows to columns
      Selection.TextToColumns _
         Destination:=.Range("A1"), _
         DataType:=xlDelimited, _
         TextQualifier:=xlDoubleQuote, _
         ConsecutiveDelimiter:=False, _
         Tab:=True, _
         Semicolon:=False, _
         Comma:=False, _
         Space:=False, _
         Other:=False, _
         FieldInfo:=Array(1, 1), _
         TrailingMinusNumbers:=True
      'Delete the columns we do not need
      .Range("B1:C1").Select
      .Range(Selection, Selection.End(xlDown)).Select
      Selection.EntireColumn.Delete
      .Range("C1:E1").Select
      .Range(Selection, Selection.End(xlDown)).Select
      Selection.EntireColumn.Delete
    End With
    If NumberSheets = 2 Then
       With MySheets(0)
     
          'Insert a row on sheet2 for headers
          .Range("A1:D1").Select
          Selection.EntireRow.Insert
   
          'Select the first column of the other created worksheet
          .Range("A1").Select
   
          'Convert the text rows to columns
          .Range("A1").Select
          .Range(Selection, Selection.End(xlDown)).Select
          Selection.TextToColumns _
             Destination:=.Range("A1"), _
             DataType:=xlDelimited, _
             TextQualifier:=xlDoubleQuote, _
             ConsecutiveDelimiter:=False, _
             Tab:=True, _
             Semicolon:=False, _
             Comma:=False, _
             Space:=False, _
             Other:=False, _
             FieldInfo:=Array(1, 1), _
             TrailingMinusNumbers:=True
   
         'delete the rows we do not need
         .Range("B1:C1").Select
         .Range(Selection, Selection.End(xlDown)).Select
         Selection.Delete Shift:=xlToLeft
         .Range("C1:E1").Select
         .Range(Selection, Selection.End(xlDown)).Select
         Selection.Delete Shift:=xlToLeft
         .Range("A1:D1").Select
         .Range(Selection, Selection.End(xlDown)).Select
   
        'filter out the duplicated data from the imported data
        .Columns("A:D").AdvancedFilter _
           Action:=xlFilterCopy, _
           CopyToRange:=Columns("F:I"), _
           Unique:=True
           .Range("A1:E1").Select
           .Range(Selection, Selection.End(xlDown)).Select
           Selection.Delete Shift:=xlToLeft
           .Range("A1").Select
           .Range(Selection, Selection.End(xlToRight)).Select
           Selection.Copy
   End With
   With MySheets(0)
   
      .Range("A1").Select
      .ActiveSheet.Paste
      .Range("A1:D1").Select
      .Range(Selection, Selection.End(xlDown)).Select
       Application.CutCopyMode = False
      .Range("A1:D26110").AdvancedFilter _
         Action:=xlFilterCopy, _
         CopyToRange:=.Columns("F:I"), _
         Unique:=True
      .Range("A1:E1").Select
      .Range(Selection, Selection.End(xlDown)).Select
      Selection.EntireColumn.Delete
      .Range("A1").Select
   End With
   ActiveSheet.ChartObjects("Chart 1").Activate
   ActiveChart.SeriesCollection(3).Select
   ActiveChart.SeriesCollection(2).Select
   ActiveChart.SeriesCollection(1).Select
   ActiveChart.Axes(xlValue).MajorGridlines.Select
   ActiveWindow.Visible = False
   Windows("Transaction Volumes by  Card Type Template.xls").Activate
   
   
   Range("C4").Select
   Do Until ActiveCell.Value = ""
   ActiveCell.Offset(0, 1).Select
   Loop
   
   Selection.EntireColumn.Insert
   Application.CutCopyMode = False
   ActiveSheet.Previous.Select
   Range("A2").Select
   Selection.Copy
   ActiveSheet.Next.Select
   Range("C4").Select
   
   'find the next empty cell in row
   Do Until ActiveCell.Value = ""
   ActiveCell.Offset(0, 1).Select
   Loop
   
   ActiveSheet.Paste
   Application.CutCopyMode = False
   
   With Selection.Font
       .Name = "Verdana"
       .FontStyle = "Bold"
       .Size = 8
       .Strikethrough = False
       .Superscript = False
       .Subscript = False
       .OutlineFont = False
       .Shadow = False
       .Underline = xlUnderlineStyleNone
       .ColorIndex = 2
   End With
   With Selection.Interior
       .ColorIndex = 49
       .Pattern = xlSolid
       .PatternColorIndex = xlAutomatic
   End With
   
   Selection.Copy
   ActiveCell.Offset(36, 0).Select
   ActiveSheet.Paste
   Application.CutCopyMode = False
   
   ActiveCell.Offset(-31, -1).Select
   Selection.Copy
   ActiveCell.Offset(0, 1).Select
   ActiveSheet.Paste
   Application.CutCopyMode = False
   
   ActiveCell.Offset(-4, 0).Select
   ActiveCell.FormulaR1C1 = _
      "=SUM(COUNTIF(Sheet1!R2C3:R65536C3,R5C2))+" & _
      "(COUNTIF(Sheet2!R2C3:R65536C3,R5C2))"
   ActiveCell.Offset(1, 0).Select
   ActiveCell.FormulaR1C1 = _
      "=SUM(COUNTIF(Sheet1!R2C3:R65536C3,R6C2))+" & _
      "(COUNTIF(Sheet2!R2C3:R65536C3,R6C2))"
   
   
   'Replace the formulas with actual values
   Range("B5").Select
   Do Until ActiveCell.Value = ""
   ActiveCell.Offset(0, 1).Select
   Loop
   ActiveCell.Offset(0, -1).Select
   Selection.Copy
   Selection.PasteSpecial _
      Paste:=xlPasteValues, Operation:=xlNone, _
      SkipBlanks:=False, Transpose:=False
   ActiveCell.Offset(1, 0).Select
   Selection.Copy
   Selection.PasteSpecial _
      Paste:=xlPasteValues, _
      Operation:=xlNone, _
      SkipBlanks:=False, _
      Transpose:=False
   Application.CutCopyMode = False
   
   'Delete the Worksheets
'    ActiveSheet.Previous.Select
'    ActiveWindow.SelectedSheets.Delete
'    ActiveSheet.Previous.Select
'    ActiveWindow.SelectedSheets.Delete
   
   Range("B41").Select
   Do Until ActiveCell.Value = ""
   ActiveCell.Offset(0, 1).Select
   Loop
   
   ActiveCell.Offset(0, -1).Select
   Selection.Copy
   ActiveCell.Offset(0, 1).Select
   ActiveSheet.Paste
   
   ActiveCell.Offset(1, -1).Select
   Selection.Copy
   ActiveCell.Offset(0, 1).Select
   ActiveSheet.Paste
   
End Sub