Another way would be to employ
Merge Many To One
This entails a small modification to the merge document (attached) and a macro (below) run from the add-in to place the check boxes. The result is in the result document example (attached). Sort the data on the customer field(attached) and that is the key field and filename field. The rest of the fields are child fields..
Code:
Sub AddChecks(oDoc As Document)
Dim oTable As Table
Dim oRng As Range
Dim i As Long, j As Long
Set oTable = oDoc.Tables(1)
On Error Resume Next
For i = 2 To oTable.Rows.Count
For j = 6 To 7
Set oRng = oTable.Cell(i, j).Range
oRng.End = oRng.End - 1
oDoc.ContentControls.Add wdContentControlCheckBox, oRng
Next j
Next i
End Sub