I have to dig into this one a bit more. There were tons of errors to fix to initially get Browserify to work, but once those were corrected the result was actually simple. The problem with assigning $ to Backbone.$ was one of the last problems, so I hacked on the code till it worked (this was definitely not the cleanest approach, but after 3 days I just wanted it to work).

To add context, the issue that I was facing is that Backbone uses this.$ not window.$. When contained in a Browserify module, this !== window, so I used this to force the assignment. 

Also, I did wrap jQuery with Browserify as well and imported it, but have not gotten it to work yet.