Looking at the way you write your functions, you clearly have not started using strict yet.

Also why is it that you must modify the array in place? That is a design decision that I look at and wonder if there isn't a cleaner solution.

But if you absolutely must get an argument in by reference and want to have a clean calling syntax, then I would throw out the thought that perhaps you want to make them into objects? Then at least you can localize the accesses to the internal structure in a semi-sane manner...