If you have the time and inclination, try this and see how you fare. You might have to make a few tweaks, it compiles clean but is otherwise untested beyond a mental run through, which given my mind is notoriously unreliable:)

sub mergeLogs {
    my ($day, @files) = @_;
    my @lines;

    foreach my $file (@files) {
        my $fh = openLogFile($file);
        warn "$0: ignoring file $file\n", next unless defined $fh;
        warn "-> processing $file\n" if $opts{'verbose'} > 0;

        while( <$fh> ) {
            next unless /Running|Dump|FromCB|Update/o;
            next if exists $opts{'day'} && ! /^$opts{'day'}/o;
            next if exists $opts{'user'} && ! /[\(\[]\s*(?:$opts{'user
+'})/o;
            
            $opts{'server'} = lc $1, next 
                if !exists $opts{'server'} && /\* Running on (\w+) -/;
            
            my $time = /(\d{2}:\d{2}:\d{2}\.\d{3})/o;
            next if exists $opts{'start-time'} && $time lt $opts{'star
+t-time'};
            next if exists $opts{'stop-time'}  && $time gt $opts{'stop
+-time'};

            s/ {2,}/ /go;
            s/ ?: / /go;
            s/^((?:\S+ ){3}).+?\[?I\]?:/$1/o;
            s/ ACK (\w) / $1 ACK /o;

            warn $_ if $opts{'verbose'} > 3;
            ## prepend the time key now save reparsing later
            push @lines, $time . $_; 
        }
        close $fh;
    }
    ## Sort in-place to save memory shuffling 
    ## (if it decides to play ball today)
    @lines = sort @lines; 

    substr $_, 0, 12, '' for @lines; ## Trim the prepended keys
    
    return \@lines;
}
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