In order to merge the CSS and JS files into one file (for each), you need to use a plugin like Autoptimize or Better WP Minify.
There’s also various caching plugins available that can help you achieve this as well.
Not sure why Autoptimize isn’t working for you – it’s one of the best in my opinion at doing this without causing issues on the site. Did you copy the settings I mentioned in the article I posted earlier in the topic?
I might be able to help further if you can link me to the site in question?