You said:

Due to the size of the list in the command line, even when I use a wildcard, I get error output like this:

-bash: /usr/bin/perl: Argument list too long
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Thus I have a problem. My input list is too long for my program to pipe in.

Maybe you did not see (or understand) the reply I made on your previous thread? (it was here: Re^3: Piping many individual files into a single perl script) An array of 100,000 file names, read from STDIN (or from a named file that contains the list), should not pose any problem, unless you have an indecently small amount of RAM (or you are wasting too much of it on other stuff). Just use a "find" or "ls" command to generate the list of file names, read that list in your perl script, and loop over it.

Your terminology in the bit that I quoted above seems confused. Using @ARGV to hold the list of file names to process (using a wildcard on the command line for your script) is not what we call "piping". Piping refers to reading from STDIN. Are you having some sort of problem with that?