Very cool. Your output doesn't quite match the OP's, but with this slight adjustment, we do:

use warnings;
use strict;

s[.{5}\K((.).(..))][$1 $2Y$3], print while <DATA>;

__DATA__
col1 col2 col3 col4 col5
1234 5678 9012 3456 7890
[download]

prints:

col1 col2 cYl2 col3 col4 col5
1234 5678 5Y78 9012 3456 7890
[download]