I did a directory comparison between 1.3.9 and IH2 with 1.3.8 as the ancestor. It looks like the following files within IH2 have changed either in IH2 or in 1.3.9:

includes/modules/additional_images.php
includes/modules/main_product_image.php
includes/modules/pages/popup_image/header_php.php
includes/modules/pages/popup_image_additional/header_php.php
includes/templates/template_default/popup_image_additional/tpl_main_page.php

Of these, the only file that has changes in BOTH IH2 and 1.3.9 is:

includes/modules/pages/popup_image/header_php.php

So, would I be correct in assuming that if I reapply all the 1.3.9 files to my shop, then merge the header_php.php file, then install IH2, I should be OK? I realize that I'll then have to do a similar exercise with Lightbox.

Thanks.