Need VBA to create new Workbook and name it based on cell value in original file

Try:

Sub CopyDataAndSave()
    Application.ScreenUpdating = False
    Dim desWB As Workbook, desWS As Worksheet, srcWS1 As Worksheet, srcWS2 As Worksheet
    Set srcWS1 = ThisWorkbook.Sheets("Detailed Outputs")
    Set srcWS2 = ThisWorkbook.Sheets("User Inputs")
    Set desWB = Workbooks.Open(Environ("userprofile") & "\Desktop\Upwork\Model_Template.xlsx")
    Set desWS = Sheets("Input")
    With srcWS1
        .Range("B8:M8").Copy
        desWS.Range("Q4").PasteSpecial xlPasteValues
        .Range("B45:M45 ").Copy
        desWS.Range("Q8").PasteSpecial xlPasteValues
        Application.CutCopyMode = False
    End With
    ActiveWorkbook.SaveAs Filename:=ActiveWorkbook.Path & Application.PathSeparator & srcWS2.Range("C14").Value & ".xlsx", FileFormat:=51
    Application.ScreenUpdating = True
End Sub

You could have a file picker window pop up where the user selects the folder and the file to open. Would that work for you? What do you mean by "it is a protected file"?