You might try a google search on "adjacency" as well. This sounds a lot like what I have run into in the IC packaging and printed circuit board industry, so those might be filters on your search as well.

Seems to me I did something like this a long time ago when I was munging test point data. I seem to recall pre-filtering to reduce the work load by finding the center of my features (boxes) and identifying those that could not possibly overlap first. It has been a long time... sorry I did not hang on to that old code. Best of luck with your project.