This pertains to the second item you bring up. I'm not 100% sure why you need to 'do it all in one go' as you say, so this may or may not be helpful. But, adapted from a node by an anonymous monk posted here, you can generate a list of directories within a specified directory.

You can use this to make your script adapt in case the number of or name of directories varies from run to run.

This:

#!/usr/bin/perl -w
use Data::Dumper;

while(<*>){
    push(@files,$_) if(-d "$_");
}
print "\n". Dumper(@files) ."\n";
[download]

will produce output like this:

sean@seanc:~/code/temp$ ls -l
total 16
drwxr-xr-x 2 sean sean 4096 2008-09-17 09:12 dir1
drwxr-xr-x 2 sean sean 4096 2008-09-17 09:12 dir2
drwxr-xr-x 2 sean sean 4096 2008-09-17 09:12 dir3
-rwxr-xr-x 1 sean sean  155 2008-09-17 09:11 dir_list.pl
-rw-r--r-- 1 sean sean    0 2008-09-17 09:12 file1
-rw-r--r-- 1 sean sean    0 2008-09-17 09:12 file2
-rw-r--r-- 1 sean sean    0 2008-09-17 09:12 file3
sean@seanc:~/code/temp$ ./dir_list.pl 

$VAR1 = 'dir1';
$VAR2 = 'dir2';
$VAR3 = 'dir3';
[download]

so you can always have an up-to-date list of subdirectories, and the code looks prettier than having a big, long hard-coded list.

Changing the '-d' to a '-f' would give you a list of files, so you could adapt that to get a list of directories, then get a list of filenames or check for the presence of a particular file.