Allow me to pour some ideas...

Use perltidy to neaten up your code a little.

Use:

use warnings;
use strict;
[download]

Is it really necessary to cd to any of these directories? If you just need to read in specific files, you can use the full path to the file.

Are the "last 3 files" based on a numeric string in the filename, or are they based on the file's timestamp?

You only need $arg=$ARGV[0]; once.