My first thought when I saw Apache::PerlRun is to simply use it. But as it turns out, it's not so great. I mean, if it were so great, then Apache would be configured in such a way. That PerlRun would run all CGI scripts ...
Apache has many ways to run perl scripts, all of them have their advantages and disadvantages. If you install mod_perl, Apache::Perlrun is installed by default. The fact that you still need to configure it doesn't mean that it's a bad option.
Also, you seem to want to embed perl in apache (that is mod_perl), but you don't want to use mod_perl (for some reason). You want to clean out all the variables and code, but you still want caching of some code, you want to use PerlRun, but you think it's bad, because it's not the default configuration.
There is no replacement for CGI if you want to run every script unmodified. If you want more speed, your programs need to take into account that they can be run more than once (i.e. that not everything is reloaded for each request).
Choose one: Apache::PerlRun (for "dirty" scripts), Apache::Registry (for clean CGI scripts - in my experience, almost all well-written CGI scripts will work with Apache::Registry) or fast-cgi (language/webserver agnostic).
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