Hi, sorry for the late response, we've been working on lots of different features. We actually decided not to include the jobs search in our main search, so that resolves one issue. The other issue with the separate jobs search, and after updating to the newest version of the plugin, I somehow got it to work properly on our development site, so I imported the search instance (after updating the plugin on development) and tested and now I'm not getting any results. At first I noticed some of the settings were different, for example some of the excluded taxonomy terms were included, so I changed that and I'm getting no results.
Also just to clarify, the customization was in order to have the categories and post types work exclusively of each other as filters if I understand correctly. That doesn't seem like we need that anymore because of the filters we are now using. If you let me know what to change back I can make the change. I do not want a customization which we may not need to be causing some of these things to be breaking.
Thank you for all your help!