Lots of folks have commented, but you've not gotten much in the way of useful answers yet, so potentially here's one.

If you don't need to transform or otherwise operate on your array as a matrix, you can use a hash of hashes, rather than an array of arrays, to represent your data. Use your indices as hash keys, rather than array indices, and you should be OK. That will suffice for plain data storage and retrieval.

If you need something fancier, then I'd once again recommend looking at the PDL extension to perl. If that's insufficient you might want to consider either some fancy games with tie and custom variables (which has some speed issues) or a different language with features better suited to the problem set. (Mathematica, Matlab, or APL all spring to mind, though I have no doubt there's some less well-known languages and software packages that are better suited to this particular problem)