Hoping there might be another FreeBSD user here who may have been through this already...
For reasons I don't want to trouble you with, I had to install the latest perl freebsd port into /usr/local/rt3/perl/ and now I need to get mod_perl to compile against that version.
Unless I miss something specific to FreeBSD ports, the whole thing should be as easy as doing:
/usr/local/rt3/perl/bin/perl Makefile.PL ... && make && make test && make install
I don't understand why are you trying to mess up with env vars at all. You obviously miss the first step, i.e. 'perl Makefile.PL'
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