Our team in finishing a project to refactor a custom form builder in our app (similar to WuFoo) and our struggles sound very similar. We are adding plugins like Backbone Relational to fight with issues, and fighting issues with the plugins... And in fact, our tech lead has actually forked Backbone (still unsure as to the exact reason). At any rate, we have shattered (what used to be) a ~1,000 line jQuery/JavaScript file into nearly 130 individual fragments of models, views, collections, templates, and helpers. Throw RequireJS into the mix... We can't be Doing It Right (TM), can we? Or are we, and I just don't get it?
[edit] spelling