Hi @pjkiley,
One way to do this, but it's not very elegant is to make two graph builder plots: 1) contour plot colored (or overlayed) with column to give color to it, and 2) scatterplot. You can then right click the scatterplot and then edit->copy frame contents, then right click contour plot and edit->paste frame contents.
If you're doing this only once or twice, then this could be a way to get what you wnat, however, this is not efficient if you need to do this many times.
Below is an example I did with the BigClass.jmp file:
You might learn how to script it out by viewing the script from the hot button.
You might be able to use the Properties(0,{Line Color(#), Fill Color(0), Item ID(:y-column, 1) within the Dispatch command to get what you want by scripting. I'm not that familiar with doing it that way, though.
I'd be interested in an elegant way to do it via scripting.
Hope this helps!,
DS