If you're using macros to build your charts, do you mind using the macros to add additional columns to your data first? You could add two additional columns, the first to have this simple code to adjust some of your data:
ActiveCell.FormulaR1C1 = "= IF(RC[-1]>999, 1000,RC[-1])"
....then fill down
Then the next column to have a simple count of data points (used later to find the point you're modifying):
Dim i as integer
Dim rng As Range
Set rng = Range("Your Range")
For Each Cell In rng
i = i + 1
cell.value = i
Next
Now plot your graph as you would with the macro, except now you're using the Adjusted Values column. And add this formatting macro:
Dim rng As Range
Dim Point As String
Set rng = Range("c2:c9")
For Each Cell In rng
If Cell.Value > 999 Then
Point = Cell.Offset(0, 1).Value
ActiveSheet.ChartObjects("Your Chart").Activate
ActiveChart.SeriesCollection(1).Select
ActiveChart.SeriesCollection(1).Points(Point).Select
Selection.MarkerStyle = -4105
With Selection
.MarkerStyle = 2
.MarkerSize = 25
.MarkerColor = 'Your Color (could base this off of the degree that it is above 1k)
End With
End If
Next
This is strong-arming the system a bit, but it would give you what you needed.
Good luck.
-ZL