Selectable Grid / Tiles

Ok this is purely for a educational / learning experience. I have been doing a lot of studying on artificial intelligence and path finding. I want to try to put some of the topics I’m learning into action but have ran into a road block right away.

Here is what I’m trying to do:
Create a grid that lays on top of my terrain(not always flat). This in its self is fairly simple and straight forward. The problem though is I want to see a few things.

1 - If anything that’s not part of the terrain is in this tile. IE: Buildings
2 - When running the A* scripts I want to see what is in its open and closed list. So would need to change the tiles to different colors for just those parts.
3 - If my mouse is over one of the projected(assuming I will use projectors) I would like to highlight it. I think this will be trivial if I can figure out #2.

Can anyone point me in the right direction? It seems that creating hundreds of 3d cubes would not be the way to go, so surely there is a different way I’m just not thinking about. There are some other post on the forums but none of them really share their solution just say they figured it out. Or maybe I am just thinking way off base.

Thanks for any assistance

I would like to know answers to the above questions as well.