Captivate 7.0 update External JS

Question

Ok, know I´m piss, I just finished tweo weeks ago a custom JS with 2.000 lines of code in jquery.
This script hide the toc, load some animations using tweenmax, load videos for intro and end of slides, among a whole bunch of other things...
Just run the update to CaPtivate 7.0 and nothing works, first, it dont recognizes the jquery on "call javascript" on the first slide and if still, I call the JS thru the modified index.html, still dont recognize the system variables.
CAN SOMEBODY TELL ME WHAT´S GOING ON????
I have lost all my work? For know I´m getting back to 7.0 insight from adobe, but I can´t have the answer that my only option is to syick with the this version, the company just bought the software, and know we was going to install on every other machine od the dept, I need realy some attention.
Thank you.

Answer 1

In my test jQuery is being called to load in the index page using an array of scripts and appends them to the head section:
var lJSFiles = [  'assets/js/jquery-1.6.1.min.js','assets/js/CPM.js','assets/playbar/playbarScript.js' ];
      cpXHRJSLoader.js(lJSFiles,function()
       //console.log("js loaded");
       lJSLoaded = true;
       constructDIVs();
     document.getElementsByTagName('head')[0].appendChild(script);
    },1);
Custom js files are loaded directly into the head and are executed first, so if you have any functions in your custom js that are using jQuery as soon as the file is loaded they won't work since the jQuery file is not in the document yet. You would need to change the way your custom js is loaded by using the window or document.ready events.