It looks as though Limbic~Region has already done much of the legwork I was about to do, and has assembled his results in this thread, which I now list here in hopes that some of the ideas therein might prove helpful.

Alternatively, Super Searching for all the reasons why Hiding your Script is nearly impossible with interpreted languages such as Perl, might also give you some ideas on how to undo what has been done by Perl2Exe.

The good news is, once you've written a program, even though much time has elapsed since then and now, the re-write is usually substantially improved.

Good luck.