Greetings,
I most likely can help you with this problem. I have 24 years programming with about 22 of that dealing with javascript and other web technologies. My concern is that there are browser based security measures that could be a problem. If you wouldn't mind messaging me with the URL of the JS file (and perhaps a brief description of what exactly it does). I can look into the issue and let you know if this is something I know how to fix, prior to you awarding the project.
Thanks,
Brett