I agree with moritz in that you might want to use another approach now that you have your string split into an array.

This sounds like it might be a job for List::MoreUtils:

use strict;
use warnings;
use List::MoreUtils qw(natatime);

my $str="AJKDHAKAESRADADKLASRRASDASDKASEKA";
my @ar = split '(?<=[KR](?!P))', $str; #to split where i ever i see a 
+K or R.
print "ar: @ar\n";

my @new;
my $it = natatime 2, @ar;
while (my @vals = $it->()) {
    push @new, (join '', @vals);
}
print "new: @new\n";
[download]

prints:

ar: AJK DHAK AESR ADADK LASR R ASDASDK ASEK A
new: AJKDHAK AESRADADK LASRR ASDASDKASEK A
[download]

Is that what you are looking for for question #1? If so, I think you can use the natatime function to also solve #2.

Update: OP has been updated.
Also, it is best if you just put code snippets inside <code> tags, rather than the bulk of your question.