use strict;
use warnings;

my $a = 'AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA';
my $b = 'ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA';

my $merged = $a;
while ($b =~ /([RYSWKMBDHV])/g) {
    my $pos = $-[0];
    substr $merged, $pos, 1, $1;
}

# $merge contains what you want
[download]

The only "unusual" thing in there is the usage of @- to get the match position.