You don't say what your "commercial package" is, but if you haven't searched CPAN yet for modules that relate to that package, you should try that. If there is a module that provides direct data i/o between a perl script and your commercial package -- or if that tool can be run via any sort of "inter-process communication" already supported by perl (cf. perlipc) -- you might be able to avoid some amount of disk i/o using a process that manages in-memory data transfer from one process to the other.

(Then again, the RAM-disk idea sounds like the easiest way to get a noticeable speed-up.)