Never use unless with logical operators. Rewrite that using if and and and not. It always looks reasonable as you're writing it, but afterwards it is unnecessarily hard to read, and when you actually are trying to debug it, you will quickly get confused in trying to work out the conditions. No, I didn't believe this advice when I was handed it. After a couple of nasty debugging sessions I recognized the limitations of my brain and took it to heart.

Other than that, most of the style things that I would fix are justified by your proposed audience.

sub wanted {
    print OUT "$File::Find::dir/";  
    print OUT "$_\n";          
    }
[download]

sub wanted {
    print OUT "$File::Find::name\n";  
    }
[download]

sub wanted {
    print OUT "Directory: $File::Find::dir\n";
    print OUT "Basename: $_\n";
    print OUT "Full Path: $File::Find::name\n";
    }
[download]

##################################
[download]

Apart from that, my initial snap reaction is that it would be better (more appealing to the novice, without being more cryptic) if there were less repetition: the two rather ugly sets of print statements that "talk to the user", each one followed by very similar-looking foreach loops, are a sure sign that you'd be better off with a subroutine that you call twice with different parameters each time. When newbies catch on to subroutines -- which is not that hard to do -- it strikes them as the coolest thing and they love it immediately. You shouldn't deny them that pleasure.

sub wanted {
    print OUT "$File::Find::dir/";  
    print OUT "$_\n";          
    }
[download]

$File::Find::dir  = /some/path/
$_                = foo.ext
$File::Find::name = /some/path/foo.ext
[download]

Other than for expository reasons, I would expect to see:

print OUT "$File::Find::name";
[download]

###selection criteria is a set of easy Regular Expressions:
foreach my $file1(@file1only) {
    unless (($file1 =~ "tmp") or ($file1=~"temp") or ($file1 =~ "recyc
+ler") or ($file1 =~ "history")) { 
        print OUT $file1;
        }
}
[download]

###selection criteria is a set of easy Regular Expressions:
foreach my $file1(@file1only) {
    unless (($file1 =~ "tmp") 
         or ($file1 =~ "temp") 
         or ($file1 =~ "recycler") 
         or ($file1 =~ "history")) { 
        print OUT $file1;
        }
}
[download]

I'm pretty sure no one uses m// anymore unless they're avoiding toothpicks (m{/lib/dir}), or obfu-ing (m atempa).

Now, are you sure you want "temp"? Because that will match "lastemployee"also. Perhaps you need "^temp$" or "\btemp\b"?

print OUT "LOWERCASING ALL FILE AND PATHNAMES BEFORE COMPARING.\n";
print "\n\n";
[download]

print OUT "IGNORING FILES WITH Tmp OR Temp IN PATHNAME.\n";
[download]

And are you comparing with the directory path, or the file path? Maybe the regex should be

$file1 =~ /\btemp\W\w)/; # temp is not the filename
[download]

foreach my $file2 (@file2only) {
  unless ( ( $file2 =~ "tmp" ) or ( $file2 =~ "temp" ) or ( $file2 =~ 
+"recycler" ) or ( $file2 =~ "history" ) ) {
    print OUT $file2;
  }
}
[download]

foreach my $file2 (@file2only) {
  unless (    ( $file2 =~ "tmp" )
           or ( $file2 =~ "temp" )
           or ( $file2 =~ "recycler" )
           or ( $file2 =~ "history" ) ) {
    print OUT $file2;
  }
}
[download]

foreach my $file2 (@file2only) {
  unless (    ( $file2 eq "tmp" )
           or ( $file2 eq "temp" )
           or ( $file2 eq "recycler" )
           or ( $file2 eq "history" ) ) {
    print OUT $file2;
  }
}
[download]

foreach my $file2 (@file2only) {
  unless ( $file2 =~ /^tmp|temp|recycler|history$/ ) {
    print OUT $file2;
  }
}
[download]

Using comments in code meant to be published seems really ugly to me (could just be me). Myself, I much prefer seeing the whole body of code (with each line preceeded with its line number), followed by a detailed line-by-line description of what is going on. It is so much easier to follow this way. So you might do something like this (I doubt my explanations are satisfactory, I just threw this together in a matter of 15 minutes or so):