Have you researched loopless coding at all? If nothing else, are you practicing sound early exit strategies?

If it's not proprietary code, or if you can slap together a pseudo version that's okay for public consumption you might paste it up to something like stackoverflow.

Nested loops are standard practice, on small datasets.

This is not that.

I'd take a peek at this wiki on nested optimization to get an idea how how you might get around it.

If not, again stackoverflow is a great resource full of expertise in things like optimization.