Pywikipedia can accept input from a few different sources.
From a list of page titles/files
From a category (if all of the affected files are already in a category)
From a page that links to the affected page titles/files. For instance, if you had a gallery page with all of the files included on it, that would work.
I can create a list of pages from the upload log. If the affected titles matched a particular pattern, I could filter the list so only the ones that matched the pattern would receive the template.
Can it be done in reverse of number 2, in which I create a category for the files we don't need changed, and the bot edits all the other files? The files don't really match a pattern, so filtering is out of the question.
The list is done, here, the template is almost done, I should have the email from Fishlabs by tomorrow, and I will finish the template and we can get the bot started.
I've finished creating the list on my end. You may want to contact Wikia vis Special:Contact on your wiki and ask them to place a bot flag on my bot account, User:I am a bot. That way, the bot won't flood the Recent Changes page while it's editing.
The bot is running now. It should take about three hours to finish (still way faster than any human). You can delete the list I created when it's done.
If you need help, feel free to leave me a message; you may also want to visit the forums or join us on Chat. You can also check our staff blog to keep up-to-date with the latest news and events around Wikia.