Edited to add: I posted this before I saw you last post.
Is the Mass upload tool an Excel tool? Maybe it would be best if we just fixed that.
Back to before editing:
I just spent the last few hours parsing and improving your code in MOD1runFirstStepofTool and I think I see the system process.
The system post the data to a web site, the "Requester" person downloads the information to (what looks like) a Worksheet. He/She also fills a Worksheet directly form the system and send them to you.
Your job is to find the discrepancies between the two sheets, which are not even close to being in the same formats, styles, or layouts.
But the real problems are in how the data is input into the system and how the system exports the data to the Web Page.
Any Way... Here is the work I've done on your code. I suggest that you run each by itself (Click inside the sub, then press F5,) to see if it works. The whole module compiles so it should work OK.
	Option Explicit
'NumberFormats used for comparing sheets
Const NmFrmtEURSign  As String = "[$€-2] #,##0.00"
Const NmFrmtUSDSign  As String = "$#,##0.00"
Const NmFrmtSimple As String = "0.00"
'Possible NumberFormats 'X, Y' & Z are commonly used as names when there are 
'no reasonable mnemonics and their usage is as limited as it is herein.
Const strX As String = "_($* #,##0.00_);_($* (#,##0.00);_($* ""-""??_);_(@_)"
Const strY As String = "_([$$-409]* #,##0.00_);_([$$-409]* (#,##0.00);_([$$-409]* ""-""??_);_(@_)"
Const strZ As String = "_([$€-2] * #,##0.00_);_([$€-2] * (#,##0.00);_([$€-2] * ""-""??_);_(@_)"
 
	Sub Main()
Sheet2PartNumSpaces
Sheet2NumberFormats
Sheet1NumberFormats
End Sub
 
	Sub Sheet2PartNumSpaces()
'Removes All Spaces from Part Number Column
  Dim rw  As Long
  Application.ScreenUpdating = False
  With Sheets("Sheet2").Columns(3)
    For rw = 2 To .Cells(Rows.Count).End(xlUp).Row
      .Cells(rw) = Join(Split(.Cells(rw), " "), "") 'SamT says, "Thank you snb."
    Next rw
  End With
  Application.ScreenUpdating = True
End Sub
 
I really should put the 'Headerless Import Duties Column code into its own sub, but it fits in with For... Next loop.
	Sub Sheet2NumberFormats()
' this first parte of this procedure gets rid of some wrong formats in sheet2,
' there are many formats that give to the cell the symbol €/$ (Accounting is one of those,or English Dollars)
' this procedures changes all Accounting USD/EUR (and others " Wrong"formats) that are used in the sheets2 into the Currency USD/EUR formats that rw want.
' All this part of the code rw did by myself :)
  
  Dim rw  As Long
  
  Application.ScreenUpdating = False
  
  With Sheets("Sheet2")
    For rw = 2 To .Cells(Rows.Count, 1).End(xlUp).Row
    ' Wrong format are replaced with correct ones ($#,##0.00 - [$€-2] #,##0.00)
    
    'Format Price Column
      With .Range("D" & rw)
        If .Value = "" Or .Value = 0 Then
          .ClearContents
          .Interior.ColorIndex = 3 'Turn the cell Red, Missing import duty.
          .NumberFormat = NmFrmtSimple
        End If
        Select Case .NumberFormat
          Case NmFrmtUSDSign 'Do nothing, Same As Exit Select
          Case NmFrmtEURSign 'Do nothing, Same As Exit Select
          Case NmFrmtSimple 'Do nothing, Same As Exit Select
          Case strX: .NumberFormat = NmFrmtUSDSign
          Case strY: .NumberFormat = NmFrmtUSDSign
          Case strZ: .NumberFormat = NmFrmtEURSign
          Case Else
            .Interior.ColorIndex = 3 'Turn the cell Red, new or missing Currency Format
        End Select
      End With
       
    'Format Freight Column
      With .Range("E" & rw)
        If .Value = "" Or .Value = 0 Then
          .ClearContents
          .Interior.ColorIndex = 3 'Turn the cell Red, Missing import duty.
          .NumberFormat = NmFrmtSimple
        End If
        Select Case .NumberFormat
          Case NmFrmtUSDSign 'Do nothing, Same As Exit Select
          Case NmFrmtEURSign 'Do nothing, Same As Exit Select
          Case NmFrmtSimple 'Do nothing, Same As Exit Select
          Case strX: .NumberFormat = NmFrmtUSDSign
          Case strY: .NumberFormat = NmFrmtUSDSign
          Case strZ: .NumberFormat = NmFrmtEURSign
          Case Else
            .Interior.ColorIndex = 3 'Turn the cell Red, new or missing Currency Format
        End Select
      End With
      
      'Headerless Import Duties Column
        With .Range("F" & rw)
          If .Value = "" Or .Value = 0 Then
            .ClearContents
            .Interior.ColorIndex = 3 'Turn the cell Red, Missing import duty.
          End If
        End With
     Next
  End With
  Application.ScreenUpdating = True
End Sub
 
	Sub Sheet1NumberFormats()
   'Change format for D & F accodingly to value in E & G WORKS! rw didn't this part of the code :(
   ' we re now working with sheet1, this procedure " reads" columns E & G and format cells in D & F accordingly
   ' the word USD/EUR in any cells of columns  E & G  triggers accordingly  the format $#,##0.00 or [$€-2] #,##0.00 for the corrispondent Cells in Columns D & F
   ' After the D & F are formatted the procedure delete columns E & G
Dim rw As Long
Application.ScreenUpdating = False
  With Sheet1
    For rw = 2 To Cells(Rows.Count, "C").End(xlUp).Row 'If you're missing a part number, you gots real problems
     
      'Set NumberForamt in Column Price
      With .Cells(rw, "D")
        Select Case .Offset(0, 1).Value
          Case "EUR"
             .NumberFormat = NmFrmtEURSign
          Case "USD"
             .NumberFormat = NmFrmtUSDSign
          Case Else
            .Interior.ColorIndex = 3 'Turn the cell Red, missing EUR/USD
        End Select
      End With
      
      'Set Number Format in Column Import Duty
      With .Cells(rw, "F")
        Select Case .Offset(0, 1).Value
          Case "EUR"
             .NumberFormat = NmFrmtEURSign
          Case "USD"
             .NumberFormat = NmFrmtUSDSign
          Case Else
            .Interior.ColorIndex = 3 'Turn the cell Red, missing EUR/USD
        End Select
        
      'Import Duties Column
        With .Range("F" & rw)
          If .Value = "" Or .Value = 0 Then
            .ClearContents
            .Interior.ColorIndex = 3 'Turn the cell Red, Missing import duty.
          End If
        End With
      End With
    Next
  
    Columns(5).Delete
    Columns(6).Delete
  End With
  Application.ScreenUpdating = True
End Sub