The webempresa.com team contacted me a couple of days ago to let me know they created a small tutorial on the installation & basic configuration of Autoptimize, including this video of the process;
The slowdown noticed when activating JS optimization is due to the relative cost of aggregating & minifying the JS. To avoid this overhead for each request, implementing a page caching solution (e.g. HyperCache plugin or a Varnish-based solution) is warmly recommended.
Muchas gracias Webempresa!