(being speed an important factor in my process?)
Are you sure? Did you actually notice that the program was too slow, or do you just think being fast might be a good thing? 5-15 elements by array is very little. So unless you process several thousands of strings, micro optimizations won't have a noticeable impact. And if you process that many strings and see that the program is slow, there might be better places to improve it than this quite basic code.
Like I said, it won't change much but one thing you can do is change
for ($ngramWindow_MIN .. $ngramWindow_MAX){
my $ngramWindow=$_;
into
for my $ngramWindow ($ngramWindow_MIN .. $ngramWindow_MAX) {
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