If the most time is spent on processing and we have no idea what kind of processing you are doing it is not easy to give you pointers. Perhaps you could put some code or pseudocode online. If not perhaps as someone else mentioned you could take advantage of the database being compiled not interpretive.

If you can arrange for your "processing" to be done at a db level you may be able to simplify the amount of perl-based processing you do. For example you might be able to use a temporary table to do things. Or as mentioned above grouping will be faster in the db.

Can you really not provide any finer resolution on the amount of time taken in the subprocesses of the "processing" step? You should be profiling everything otherwise how are you going to find where the bottleneck is in the code?