corcra:

A couple notes:

• The "Use of uninitialized value" error may just be due to blank lines in (or at the end) of your file(s). Often, when I'm debugging file readers, I'll print the line read just before processing it during development, and print the values at various locations in the code.
• Arrays in perl are 0-based. I mention that because it looks like you're using the third column of File2 as your line identifier, but your data indicates that the second column would be a better choice. (Again, printing the values in your loops would help you see that stuff.)

While I'm advocating that you add a few print statements during development, you don't need to leave them in when your code works. So don't be afraid to put in a few prints here and there. (I tend to use a prefix on the print strings to help me figure out what's printing and why. Something like:

while (my $line = <DATA>) {
   chomp $line;
   print "$.: $line\n";   ###
   my ($x, $y, $key, $bar) = split /,/, $line;
   print "A: x=$x, y=$y, k=$key, b=$bar.\n"; ###
   if ($key =~ /[^\d]/) {
      print "BOOM: non-numeric key value <$key>\n"; ###
      ... stuff ...
   }
   else {
      print "B: plover=...\n"; ###
      ... other stuff ...
   }
}
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Putting the prefixes on your lines lets you use grep (or equivalent) to dig through your output to find lines of interest. For example, I may run my program and check for non-numeric keys like this:

perl foobar.pl >tmp
grep -E '^BOOM:' tmp | wc -l
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When I'm happy with a section of code, I tend to comment out the print statements, and when it all works as I like it, I go back and delete them (the lines marked ###).

Finally, notice that after every variable in a print statement, I have a graphic character (., >, etc.) so I can see if the string has trailing blanks, carriage returns, etc.

...roboticus

When your only tool is a hammer, all problems look like your thumb.