How can I make this userform timer faster?
Just formatting first:

Your code is missing indentation and has some extra newlines in it. 

Your Do Until loop should be double indented because it is inside of a sub.
You should also get rid of the extraneous commented code. If you got it working, get rid of the junk.

Here is what the code should look like:

Dim StopTimer As Boolean
Dim Etime As Single
Dim Etime0 As Single
Dim LastEtime As Single
Dim goal As Single
Dim Etime1 As Single
Dim Etime2 As Single
Dim LastEtime2 As Single

Public Sub btnReset_Click()
    StopTimer = True
    Etime = 0
    Etime0 = 0
    LastEtime = 0
    Etime1 = 0
    Etime2 = 0
    LastEtime2 = 0
    lblTime.Caption = "00:00:00"
    lblExtra.Caption = "00:00:00"
End Sub

Public Sub btnStart_Click()
    goal = 86400 * (Sheets("Input").Range("C2"))    'goal time in seconds
    StopTimer = False
    Etime0 = Timer()
    Etime1 = Timer() + goal
    Do Until StopTimer
        If Etime &lt; goal Then
            Etime = Int((Timer() - Etime0) * 100) / 100
            If Etime &gt; LastEtime Then
                LastEtime = Etime
                lblTime.Caption = Format(Etime / 86400, "hh:mm:ss")
                DoEvents
            End If
        Else
            Etime2 = Int((Timer() - Etime1) * 100) / 100
            If Etime2 &gt; LastEtime2 Then
                LastEtime2 = Etime2
                lblExtra.Caption = Format(Etime2 / 86400, "hh:mm:ss")
                DoEvents
            End If
        End If
    Loop
End Sub

Public Sub btnStop_Click()
    StopTimer = True
End Sub

Public Sub ComboBox1_Change()
    Dim cotime As Single
    Sheets("Input").Range("A2") = Me.ComboBox1.Value
    Me.AvgTime.Caption = Format(Sheets("Input").Range("C2"), "hh:mm:ss")
End Sub

Public Sub ComboBox2_Change()   
    Sheets("Input").Range("B2") = Me.ComboBox2.Value
    Me.AvgTime.Caption = Format(Sheets("Input").Range("C2"), "hh:mm:ss")
End Sub


Private Sub UserForm_DblClick(ByVal Cancel As MSForms.ReturnBoolean)
    Application.Visible = True
End Sub

Private Sub UserForm_Initialize()
    ComboBox2 = ""
    ComboBox1 = ""
End Sub


It is a lot easier to read this way as well.



Your naming should be "pascalCase" for everything.

Lose the Hungarian notation on the labels; name the labels appropriately, like timeOutput or something like that.


StopTimer -> stopTimer
Etime -> eTime
LastEtime -> lastETime