Use the Editor to open the bfa_custom_comments.php file. Add the following after about line 4 (the "global $bfa_ata" line):
global $mycommentnumber; $mycommentnumber=0;
echo "(# " . $mycommentnumber . ") ";
Then edit the "comments.php" file. After about line 12 (where it says "You can start editing below"), add these two lines:
global $mycommentnumber ; $mycommentnumber = 0;
echo "<div class = 'mycommentnumberstyle'>(# " . $mycommentnumber . ") </div>";
Of course, make a backup copy of the files before you edit them, and save a copy of the changes somewhere so you can re-do them in case of a update.
Enjoy: it's not fancy, but it will work.