Hello William,
Guess you have been able to find a breakthrough!
The ERE plugin is very robust and flexible, you just have to give it some time to understand how the layout or bootstrap works since it was designed with the later.
If you’re using a non bootstrap theme, then there will be no need disabling the bootstrap files from the plugin since those files are needed by the plugin.
Another thing you can do is to override the existing plugin templates. This article from the plugin author will guide you.
One of the main issues that was breaking my layout were the following files: wrapper-start, wrapper-end. you can find them at plugins/essential-real-estate/public/templates/global. Since i use a bootstrap theme, the above files were attending what my theme had already added.
Generally, you have to do some overriding to get the desired result for your project.
If you believe the current update is breaking your entire site, you can download older versions of the plugin here and test to see if your problem will be solved. When you open the link, scroll to the bottom of the page to access older versions of the plugin.
My advise generally will be, if you’re able to fix the issue, you have to thoroughly test future updates on a development server before running it on the live website.
For the past week, the plugin authors have been releasing constant updates which i believe will get the plugin stable again.
For this plugin: Asset CleanUp: Page Speed Booster, it’s fantastic and can improve the overall performance of your site since it enables you to load scripts only on the pages needed. I’m ditching Autoptimize for it.
Wish you luck!
Warm regards.