Just some BS'ing...brainstorming or bullsh*ting...take your pick. :-)
I'm not sure what the Quad tree is used for, and whether you really need it, but as far as overlooking something, I would wonder if it is the fastest way to get your lists. Might not it be faster to make AoA's (arrays of arrays), and loop thru them with Inline-C, finding all $states==1, then extracting the $x,$y,$z.
I'm just mentioning it, because if your grid gets larger, and you are doing 3d stuff, you will need speed. Perl is relatively slow doing recursive math calculations.
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