(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 $ngramWindow=$_;
[download]

into

for my $ngramWindow ($ngramWindow_MIN .. $ngramWindow_MAX) {
[download]