May I ask how you are using the suffix array you are constructing? (Perhaps a short example?)

I ask because, as you've discovered, constructing suffix arrays in Perl -- as opposed to C or other languages where you can manipulate pointers to avoid large scale memory duplication -- is an expensive operation, and in the past I've found that then using them also carries high costs.

Generally, I've found that there is usually a different approach to the underlying problem that works out substantially more efficient by avoiding the construction of the suffix array.