All I learned from that about the big picture is that you are dealing with coordinates and you have some (undisclosed) way of making a key from the coordinates for each "something" you want to store. I still have no idea about what you actually want to store in a hashy thing, nor what you intend to do with it once stored.
Without know what you want to eventually do with this stuff, I still think using a database (DBI and DBD::SQLite) is likely to be a good solution to the problem. But, again, if you can mock up something close to your real problem in 30 or so lines (fudge the calculations etc.) then we can probably give you a good starting point for the data management code.
True laziness is hard work