Apparently there is a rather small limit on post size for these forums ... here is more info:
For anybody else having this problem I found http://requirejs.org/docs/optimization.html#onejs
to be really useful. Here is the file I am using with my bundle options for anybody who needs to do something similar:
In node I can just run r.js -o require_bundle.js at the root of my application (once I export and extract it to my hard drive). I then just upload the main-built.js file and include that file instead of requireJS at the end of my index.html file.