Adam, I’m glad to hear none of the core code from our plugins was modified.
I’d suggest being on the current versions of WordPress and all our plugins and switching to a WordPress default theme like Twenty Fifteen.
Then add your customizations in stages to see which customizations break your site. Once you figure them out, please report back and we can probably help you know how to update your code for the latest versions.
I hope this goes well for you. Please let me know.