If the positions of all the characters are very strict you may be able to write a program to determine those positions. Once you have those positions you could proceed with parsing the 'scan' lines. Here is a small code excerpt that you could use:

use strict ;
use warnings ;

my @pins = qw(31 22 13 84 95) ;
my @positions = (40,42, 44, 46, 48) ;

while (<DATA>) {
    my $line = $_;
    my $scan ;
    my $offset ;
    if ( $line =~ /(scan\d+)\s*(\d+)/ ) {
        $line = $line . <DATA> ;
        $scan = $1 ;
        $offset = $2 ;
    }
    for my $i (0..$#positions) {
        $_ = $positions[$i] ;
        my $pin = "p" . $pins[$i] ;
        if ( $line =~ /^.{$_}([HL]).*?\n.{$_}[\^]/ ) {
            print "$scan $offset $pin $1\n" ;
        }
    }
}

__DATA__
scan1        2965                       H L H L H
                                            ^
scan2        2200                       L H H L H 
                                          ^
scan3        1100                       H L L L L 
                                          ^
scan4        1500                       L L H H H 
                                            ^
scan5        2800                       H H L H H
                                          ^     ^
[download]

Output:

scan1 2965 p13 H
scan2 2200 p22 H
scan3 1100 p22 L
scan4 1500 p13 H
scan5 2800 p22 H
scan5 2800 p95 H
[download]