I'd agree with some of the previous suggestions that Permaculture is a values-based design approach... a set of principles. so you are not studying a "permaculture farm", but making comparisons between agroecological systems that to a greater or lesser degree follow PC principles (or any other ecological design principles). Agroforestry research is where you'll find peer reviewed studies on polyculture vs. monoculture, and the efficiecies of intercropping... a good summary might be
http://www.amazon.com/Agroforestry-Soil-Management-Anthony-Young/dp/0851991890 or
http://www.amazon.com/Temperate-Agroforestry-Systems-Andrew-Gordon/dp/0851991475/ref=sr_1_1?s=books&ie=UTF8&qid=1355544909&sr=1-1&keywords=temperate+agroforestry+systems -- and be ready to pay peer reviewed prices.
A central principle of Permaculture is that a viable system must store more energy than necessary for its construction, and so you start getting into ecological accounting and energetic analysis. On this front the foolishness of industrial agricultural systems is self-evident.. they deplete soil by burning fossil fuels. Don't need to look far for evidence.
If you are looking for human labor efficiency, rather than dollar per calorie, I have not see PC compete, because the dollar economy is so very good at externalizing costs. You just have to pick your units.
Consider The World Bank for example...
http://dotearth.blogs.nytimes.com/2010/10/28/world-bank-pushes-to-include-ecology-in-accounting/
So ecosystem service markets are a tricky thing, but are growing rapidly, for example the EU has begun shifting its agricultural subsidy system from commodity supports to paying farmers for providing public services.
All these are examples of the world very slowly coming in line with what Permaculture was talking about thirty years ago.
