@maxonline my sincere apologies for not getting back to you sooner! Please use only one tool to combine JS. If you are already doing it via Avada, then keep it that way if it works fine. Just don’t also enable the same feature in WP Rocket and Asset CleanUp Pro.
Whenever you test the website in Google PageSpeed Insights and other tools and you wish. to clearly view the unused CSS & JS, please append a random string such as /?random123 to the URL. This way, the tool will load the non-cached version of the page and each CSS/JS file will be loaded individually, instead of viewing the report for one combined file. Some CSS files, for instance, have 100% of unused CSS and you can determine if you can unload it or not, in the end reducing the total size of the combined files (if you keep unloading files that are not needed on the targeted page).
Yes, you can exclude JS files from the combination by using the text area field below “Do not combine the JavaScript files matching the patterns below (one per line, see pattern examples below):” from Asset CleanUp’s “Settings” -> “Optimize JavaScript” -> “Combine loaded JS (JavaScript) into fewer files”.
As for the broken layout (e.g. drop-down menu and grid layout), that could be from an unloaded CSS file that is essential and shouldn’t be unloaded or, if you enabled “Combine CSS”, there could be a file that needs to be excluded from the combination list, this is one is rare, but it could happen).
Please re-activate the plugin in “Test Mode” (this way your visitors won’t be affected) and I could skip it via /?wpacu_skip_test_mode (so only myself would view any broken layout) and find out the culprit.