I do not know the exact answer to your question since while having used Perl in Japanese environments it is not jperl. However I can point you in a couple of directions.

I just got an email announcement (in Japanese, tell me if you want to see it) from Masayuki Moriyama (moriyama at miraclelinux.com) that he has published Encode::ISO2022JPMS, apparently part of a bounty to convert legacy encodings for perl and some other systems, which allows ISO-2022-JP-MS to be used on perl 5.8.x. See http://sourceforge.jp/projects/legacy-encoding (and click the Project Homepage link to see the Wiki (in Japanese). The email specifically mentions conversion of CP932 and some popular double byte Japanese symbols like the wide tilde mark. May be needed for your file names.

Also I think you may not be alone in this and you should probably send an email (English is okay) to one of the best known encoding guys, Dan Kogai (maintainer of the Encode module. Incidentally I was reading the Encode::PerlIO pod and while it looks like you can do wild encoding on a filehandle I can't tell what happens to filenames. Encode claims to provide a layer that can alter encodings, which if true might be good for you.

Anyway, I hope this is not worse than useless but as someone mentioned altering the course of perl itself, I think you ought to talk to the people like Dan who work hard on making the world safe for Japanese perl programmers, or vice versa. Anyway I presume you know all this stuff but before diving into the guts of it you might like to ask (if you haven't already) the Japanese guys what they think. They may also throw their hands up in the air though.. good luck. My guess is you should just buckle down and rewrite all those programs. It is easier I think than changing perl and maybe having to check if your deep mods continnue to work in future versions of perl.

Matt