Yes, it makes sense.
Its possible that you can do a rough transformation assuming a linear relationship at least within the grid that your doing the coordination transformation. Error will be introduced, and the amount of error will be based on the size of the transformation grid.
The first question is where on the 2D map do the waypoints appear, and how is the lat/long information stored for those waypoints? Similarly, when and how is the inch information represented on the 3D map? And are the waypoints mapped to each other. In other words, for each lat/long waypoint on the the 2D map is there a correspondong waypoint in inches on the 3D map?
Also, when the 2D mapped is clicked, how do you know the location where the click occurred, and what is the basis point for the click coordinates? Do you have the location in the click coordinates of any of the waypoints on the 2D map?
There are several different approaches, and the answers to these question will hopefully provide some indication of what would be the most efficient approach. Good Luck
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As a circle of light increases so does the circumference of darkness around it. - Albert Einstein