This macro appears to do what you asked for...

Sub AlignColumnData()
Dim M As Long, D As Long, Rw As Long, Main As Variant, Data As Variant
With WorksheetFunction
Main = .Transpose(Range("A1:A" & Cells(Rows.Count, "A").End(xlUp).Row))
Data = .Transpose(Range("B1:B" & Cells(Rows.Count, "B").End(xlUp).Row))
End With
Range("A:B").Clear
M = LBound(Main)
D = LBound(Data)
Do While M + D <= UBound(Main) + UBound(Data)
Rw = Rw + 1
If Main(M) = Data(D) Then
Range("A" & Rw).Resize(1, 2).Value = Main(M)
M = M + 1
D = D + 1
ElseIf Main(M) < Data(D) Then
Range("A" & Rw).Value = Main(M)
M = M + 1
Else
Range("A" & Rw).Offset(0, 1).Value = Data(D)
D = D + 1
End If
Loop
End Sub

Rick Rothstein (MVP - Excel)