I think it should go like this:

In fact, corn is such a poor source of ethanol that researchers at the University of Minnesota estimate that converting the entire U.S. corn crop — the sum of all our ears — into ethanol would replace only 12 percent of our gasoline consumption of which 3% would be new BTUs and 9% from conversion of coal, natural gas and oil.

I don't entirely agree with this point either:

So some of the ethanol flowing out the back end of the ethanol plant must be rerouted around to the receiving dock to make more ethanol.

We don't demand that other energy systems are self sufficient. No one says a windmill must be be only constructed using energy from wind. There are good reasions why the ethanol should, and eventually probably will, be rerouted around to the receiving dock. Once adequate scale exists, it should be possible to construct farm equipment that runs on hydrous ethanol. In this configuration, engines get nmore output from the same BTUs, EROEI would improve from reduced transportation of fuels, and hydrous ethanol can have water content of 5% or so, reducing energy wasted in distillation.

However, in the meantime, any requirement that ethanol facilities use only ethanol for their fuel input is impractical for reasons that have nothing to do with the theoretical utility of the exercise.