...does anyone know of a good module for doing the permutations...
Algorithm::Permute and NextPermute() from tye's Algorithm::Loops module are both very good implementations.
I think that the idea of generating a signature could be made to work well for your application. I saw the extra information that you posted in reply to tachyon and I think I see the problems your describing, and also some of a possible solution. The key to taking the thoughts further is having some test data to work with. If you felt like placing some on your doowah2004's scratchpad, and /msg'ing me, I enjoy playing with it.
That said, I'm still not entirely sure that I understand the full scope of the problem, so maybe I should just accept your more informed judgement on the matter :)
Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"Think for yourself!" - Abigail
"Memory, processor, disk in that order on the hardware side. Algorithm, algorithm, algorithm on the code side." - tachyon
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