The two phrase macros could be simplified since they are reading the same source file. This would speed up your execution time by a considerable amount.
Then you can also reduce the total amount of code by making the macro into a function (or sub) with inputs. Note that this reduces the amount of code you have to maintain but won't be faster to execute.
Code:
Sub QC_Time()
HighlightPhrases MyAcroFileName:="C:\Users\gontch\Desktop\Phrase Running List.txt", bAll:=True
HighlightPhrases MyAcroFileName:="C:\Users\gontch\Desktop\Acronyms Running List.txt", bAll:=False
End Sub
Function HighlightPhrases(MyAcroFileName As String, bAll As Boolean)
Dim MyString As String, rng As Range
Application.ScreenUpdating = False
Open MyAcroFileName For Input As #1
Do While Not EOF(1) 'loop through the file until the end of file marker is reached
Line Input #1, MyString 'read line of text, place it in the MyString variable
Set rng = ActiveDocument.Range 'Reset the Range object to the entire current document
With rng.Find
.Text = MyString
.Replacement.Text = MyString
.MatchCase = False
.MatchWholeWord = True
.Forward = True
.Replacement.Highlight = True
If bAll Then
Options.DefaultHighlightColorIndex = wdPink
.Execute Replace:=wdReplaceAll
End If
Options.DefaultHighlightColorIndex = wdYellow
.Execute Replace:=wdReplaceOne
End With
Loop
Close #1 'close the text file
Application.ScreenUpdating = True
End Function