First of all, Sort that code......... Gather all javascript Library into one project. Separate and try to understand, which JavaScript Files and its functions used in Which Entity Forms on what event.
One you Map those functionality, try Managing the Code using JQuery or any other library you are comfortable with.
There is no recommended path which one is best, but XRM framework is the Native CRM 2013 that we should use and additionally JQuery/Kindo/Angular...whatever you feel comfortable with.