Untested, but you need to refer explicitly to the sheet you're talking about (using Cells for example - cells of which sheet?).

[vba]
Option Explicit
Sub SortAndColor()
Dim LastRow As Long, Rw As Long, a As Long
Dim MySheets() As Worksheet

MySheets = Array("Master", "Seaport-e")

For a = LBound(MySheets) To UBound(MySheets)
With Sheets(MySheets(a))
LastRow = .Cells(.Rows.Count, 7).End(xlUp).Row

For Rw = LastRow To 2 Step -1
If .Cells(Rw, 7).Value <= "09" Or InStr(.Cells(Rw, 39).Value, "*If chosen") > 0 Then
.Cells(Rw, 1).EntireRow.Delete
Else
Select Case .Cells(Rw, 39).Value
Case "Contract Awarded": .Rows(Rw).Interior.ColorIndex = 35
Case "Part A Held": .Rows(Rw).Interior.ColorIndex = 34
Case "Part B Accepted": .Rows(Rw).Interior.ColorIndex = 38
Case "Part B Submitted": .Rows(Rw).Interior.ColorIndex = 36
Case "Planning": .Rows(Rw).Interior.ColorIndex = 2
Case "Postponed": .Rows(Rw).Interior.ColorIndex = 39
End Select

.Rows(Rw).Font.ColorIndex = 1
.Rows(Rw).Borders.LineStyle = xlContinuous
End If
Next Rw
End With
Next a
End Sub
[/vba]