Question: how can I invoke Perl from the command-line so that these file-handles are properly initialized?

For any CGI program, setting the environment and STDIN with the right values should do it. I'm not sure if CGI.pm has any provisions for doing upload debugging, though it does pass command-line parameters to the script as if they're normal param()s if you don't do anything to the environment.

I'd not be very surprised if there was a module on CPAN that would do this for you, but I never searched for one.

See RFC 3875 or earlier.