There are some fairly dubious coding practices in there, and I don't yet guarentee it solves every puzzle, but it does solve the (now removed) example.

I'll try test it a bit more and clean it up a bit.

#! perl -slw
use strict;

sub uniq { my %x; @x{@_} = (); keys %x }

my $len = shift @ARGV;

my $re = '^';
my $c = 0;
for my $i ( 0 .. $#ARGV ) {
    my( $word, $common ) = split ':', $ARGV[ $i ];
    die "Bad arg '$ARGV[ $i ]'" 
        unless $common >= 2 and $common <= length( $word );
    my $uniq = join'', uniq( split '', $word );
    $re .= "(?=(?:.*?[^$uniq]){${ \ ($len - $common) }})";
    $c++;
    $re .= "(?=.*?([$word]).*?(?!\\$c)";
    $re .= "([$word]).*?(?!" 
        . join( '|', map{ "\\${ \ $c++ }" } 0 .. $common-2  ) 
        . ')'  and --$c 
        if $common > 2;
    $re .= "[$word])";
}
$re .= '.' x $len . '$';
$re = qr[$re];

my %w;
open W, '<', 'words' or die $!;
m[^[a-z]+$] and push @{ $w{ length() } }, $_ while chomp( $_ = <W>||''
+ );
close W;

my @m = grep{ $_ =~ $re } @{ $w{ $len } };
print ~~@m;
print for @m;
__END__
P:\test>421692-1 5 bumps:2 seams:2 domes:3 shake:3 pokes:3 dukes:3
1
house
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