I think one problem is the libraries are loaded before the variables are made available but putting them in BEGIN breaks stuff.

I wonder what exactly you have tried, and how BEGIN did break stuff. As you suspected, initialising the variables in a BEGIN block should work to get the values passed to the lib.

A heavily simplified snippet might help ($foo represents $LOGFH etc. that you want to pass to the lib):

#!/usr/bin/perl -w
use strict;

my $foo;
BEGIN { $foo = "bar" }
use License ($foo);
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with License.pm being

package License;
use strict;
my $foo;

sub import {
    shift;
    $foo = $_[0];
    print "foo = $foo\n";
}
1;
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should print "foo = bar" when the main program is being run.

Note that $foo has to be declared outside of the BEGIN { }, because the latter implies an extra block scope.

Another way would be to use require instead of use and call the import method explicitly:

my $foo = "bar";
require License;
License->import($foo);
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In this case, the three statements would be executed at runtime in the sequence they appear, so $foo would be properly initialised before the import method is being called.