Although by comparison lookahead and behind might get better performance because of less passes per line of text, sauoq's idea of simply removing the exceptions, which became just a few lines inserted into the orginal code still managed to performed very well indeed (still only a second or two through the whole tree). Notice that $_ is getting all the exceptions removed from it cumulatively, i.e. including for other search strings, but that doesn't do any damage given that the parameters of the problem already preclude one search string being a substring of another by reductio ad absurdum.

sub SmartSearch {
    my $srch = shift;
    my $eref = $_{ EXC }{ $srch };
    for my $exc ( keys %$eref ) {
        s/$exc//g;
    }
    return /$srch/;
}
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