@katinkamom What problems currently exist in your game with no mods or custom content present? I understand you don't want to play like that in general, but it's a critical test—troubleshooting other aspects of the game isn't going to fix a mod-related issue, and vice versa.
The XML Injector is probably not the issue here. When you remove it, mods that depend on it stop working too, meaning if they're broken or outdated, they're not affecting your game anymore. Some mods do not depend on the XML Injector and would still work (or not) as usual.