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the file in question is not in a directory where over rides exsist, as I stated above.

so you will need to make the changes in
includes/modules/pages/checkout_success/header.php

and keep good...

you are going to want to ues includes/modules/pages/checkout_success...

but earlier you stated that you will manually generate the code....

if your doing this manually why worry about...

It wont parse it from the comments,
after they hit confirm they can add anything to that section anyway....

I use it for all kinds of things.,
usually tracking codes and such

If your manually generating the code then just put the code in the comments section of the exsisting order.