It's been more than a year since you've posted this workflow. How is it working out for you? It's better than anything I've been able to come up, but it's still quite complicated and I'm sure if I implement it I will likely fall back on other habits. I'm interested to hear how useful/easy you've found it and whether you are sticking to it still, or if you've found a better solution.
I love evernote for it's search, gathering and organizing capabilities, but I prefer zotero for my references because of the automatic metadata and Word integration. If only they can be efficiently combined in the way you describe conceptually.