I am also running W3 Total Cache. My settings in Striking>Advanced are:
Combine Js: Off Combine CSS: Off Move Js to bottom: On
If I switch on Combine CSS/Js, my site breaks.
On W3 Total Cache I keep Minify CSS On but I must keep Minify Js Off, as it prevents my slideshow from working. I am really looking forward to finding the way to minify Js as it is the only thing that is stopping my site from having a score of 97 instead of 87 running Google Page Speed Test.
Kappy recently replied to all those questions about this in another thread. But if the site breaks leave them off. And he also adviced to use another minify plugin.