Thanks for your help. I've updated the code as follows, and now, on that same line I'm gettting this error:

"Run-time error '1004':

Cannot run the macro 'Model Manager Extract Companion.xlsm!CallD2ResultsFunction'. The macro may not be available in this workbook or all macros may be disabled."

Private Sub CommandButton3_Click()
Dim OtherBook As String
Dim ProjDir As String
Dim ProjOutDir As String
Dim ResultsFile As String
Dim i As Integer
Dim j As Integer
Dim ManageArray() As String
Dim LastCol As Integer



'get values for project directory, output folder, batch numbers, batch run labels,
'output file names, results filename, weather file

With Sheets("Manage")
    ProjDir = .Cells(4, "G").Value
    ProjOutDir = .Cells(5, "G").Value
    ResultsFile = .Cells(6, "G").Value
End With

With Sheets("Batch Runs")
    'Get last column:
    LastCol = .Cells(3, .Columns.Count).End(xlToLeft).Column
    'Fill an array with run number, base filename, batch run label, and location
    Debug.Print LastCol
    ReDim ManageArray(1 To LastCol - 1, 1 To 5)
    For i = 1 To LastCol - 1
            ManageArray(i, 1) = i
            ManageArray(i, 2) = .Cells.Find(What:="RUN", After:=.Cells(1, 1), LookIn:=xlValues, LookAt:=xlPart, SearchDirection:=xlNext, _
            MatchCase:=True, SearchFormat:=False).Offset(0, i)
            ManageArray(i, 3) = .Cells.Find(What:="Base Filename", After:=.Cells(1, 1), LookIn:=xlValues, LookAt:=xlPart, SearchDirection:=xlNext, _
            MatchCase:=True, SearchFormat:=False).Offset(0, i)
            ManageArray(i, 4) = .Cells.Find(What:="Batch Run Label", After:=.Cells(1, 1), LookIn:=xlValues, LookAt:=xlPart, SearchDirection:=xlNext, _
            MatchCase:=True, SearchFormat:=False).Offset(0, i)
            ManageArray(i, 5) = .Cells.Find(What:="Location", After:=.Cells(1, 1), LookIn:=xlValues, LookAt:=xlPart, SearchDirection:=xlNext, _
            MatchCase:=True, SearchFormat:=False).Offset(0, i)
            
    Next i
    
    Debug.Print ManageArray(1, 1)
    Debug.Print ManageArray(1, 2)
    Debug.Print ManageArray(1, 3)
    Debug.Print ManageArray(1, 4)
    Debug.Print ManageArray(1, 5)
    Debug.Print ManageArray(2, 1)
    Debug.Print ManageArray(2, 2)
    Debug.Print ManageArray(2, 3)
    Debug.Print ManageArray(2, 4)
End With

'open eQuest extract file, rename it, and put the data onto sheet 2
'test if the file exists first.
'Debug.Print ProjDir + "\" + ResultsFile
If Len(Dir(ProjDir + "\Model Manager Extract Companion.xlsm")) > 0 Then


    Workbooks.Open Filename:=ProjDir + "\Model Manager Extract Companion.xlsm"
    OtherBook = ActiveWorkbook.Name
    
    With Sheets("Manager")
        .Cells(4, "B").Value = ProjDir
        .Cells(5, "B").Value = ProjOutDir
        .Cells(6, "B").Value = ResultsFile
        
        For i = LBound(ManageArray, 1) To UBound(ManageArray, 1)
            .Cells(8, i + 1).Value = ManageArray(i, 1)
            .Cells(9, i + 1).Value = ManageArray(i, 2)
            .Cells(10, i + 1).Value = ManageArray(i, 3)
            .Cells(11, i + 1).Value = ManageArray(i, 4)
            .Cells(12, i + 1).Value = ManageArray(i, 5)
            .Cells(13, i + 1).Value = ManageArray(i, 3) + " - " + ManageArray(i, 4) _
                 + " - Baseline Design"
        Next i
    End With
    'call the function in the Model Manager Extract Companion
    'Debug.Print ProjDir + "\" + "Model Manager Extract Companion.xlsm!CallD2ResultsFunction"
    Application.Run "Model Manager Extract Companion.xlsm!CallD2ResultsFunction"
Else
    'File does not exist
    MsgBox "Model Manager Extract Companion.xlsm not found.  Please ensure you have a copy of this file with this name in the project folder listed on the model manager."
End If