I feel your pain with JS dependency resolution and management, I have yet to get it with grunt, either. I solved that problem with RequireJS. Have you given that a shot?

RequireJS is incredible when it comes to managing dependencies and organizing JS code in general. Combine it with a requirejs task in Grunt to automatically optimize your JS code and you've got a real slick development-to-production JS pipeline on your hands.

Granted, RequireJS may seem a little funky at first, but I promise you taking the couple of hours necessary to learn its basics will make your life (at least when it comes to developing JS) much easier.