[Steven Zahm]

@ josh901

This is one of the pages I referenced when setting up W3TC:
http://www.inspire2rise.com/w3-total-cache-settings.html

This page seems to do an ok job at how to manually add JavaScript files:
http://uprankers.com/w3-total-cache-javascript-minification-troubleshooting/

This part is very tedious as it requires testing after adding each one. And then after plugin/theme updates you have to really give your site a good once over because an update to a JavaScript file could break if it will be able to be minified or not.

Hope that helps.