Of course, you can search within the custom fields created by ACF. On the General Options -> Sources panel you can choose which custom fields to search within. I see you already did that.
Basically if you remove the custom field filters, and turn off the front-end options alltogether, it will simply search those fields without filtering and return results based on them. In this case don't forget to change the search shortcode on the front-end back to the default one.
If you like my products, don't forget to rate them on codecanyon :)