For the record; I wans't trying to be "nozey", or anything. But I found it hard to speak specifically to solution(s) w/o a bit more info. :)

As I mentioned in my original response to your question; isn't it enough to simply tell your Perl applications which Perl to use? I'm thinking "shebang" here, but I know many of the other stuff allows you to setup any desired ENV you might/may require.

As I await your response, I'll go dig up all the old links I have for httpd.conf related stanza's I recall having seen, a couple, or so years ago, and update this post, or reply as appropriate.

--Chris

UPDATE:
I think the following covers what I had recalled, pretty well:
perl-apache-httpd-conf
P.S. Just for the record; you can do all of this on VirtualHost basis, meaning; a different host can run a different Perl -- my own recollection.