Not sure of the best way to do this. But there are a number of less ambitious ways than you have tried.
I would delete the duplicate comment template, and instead you make use of the following piece of code. I haven’t tested it, but it should work. Change the category IDs in the code to match the categories you want to customize the instructions for, then put it in your theme.
//if the category ID is 1 or 2 do something
<?php if ( in_category(1,2) ) { ?>
//if the category ID is 1
<?php if ( in_category(1) ) { ?>
//Show the following text
<p>This is your instructions for posting comments.</p>
//if the category ID is not 1, it must be 2
<?php } else { ?>
//so show this text
<p>This is your instructions for posting comments.</p>
<?php } ?>
//if the category ID is not 1 or 2
<?php } else { ?>
//show the default text
<p>This is your defualt instructions for posting comments.</p>
<?php } ?>