I have not seen any reference that describes exactly WHERE the energy/fossil fuel is used to make biofuels. This is an important part of the argument.

Some things, like drying corn or running irrigation pumps, could be switched to alternative power sources, like solar or nuclear. Others, like fertilizer manufacture, are a different question. I think (haven't researched it) they crack the chemicals for ammonia from natural gas, as well as the energy, which implies a chemical resource problem, not just an energy one. But if you have enough electricity available, from nuclear or other non-hydrocarbon sources, you can make pretty much anything from anything.

You're point on the energy balance of making, say, gasoline is a very good one. I don't know how much energy goes up the pipes in a refinery. More research, and I'm not getting paid for this!

I would like to see a really comprehensive study on this, including these factors, and I haven't yet.