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Nate, I'd be very interested in reading your paper when it is released.
I'm curious how you derived some of the figures you have in your example. I can't replicate what is often offered as energy balance of a (theoretical) cellulosic ethanol plant when tracking the mass balance of the plant.
Take 1 kg of switchgrass for example.
It's 42% cellulose, 31% hemicellulose, and 27% lignin (including 0.7% ash).
From the cellulose, assuming 100% recovery, the stoichiometric ethanol yield of 51%, and 75% fermentation efficiency of glucose, you get 0.16 kg (0.20 l) of ethanol, 0.21 kg of CO2, and 0.05 kg of other mass (additional bacteria body mass; dilute solids)
From the hemicellulose, assuming 100% recovery, and 50% fermentation efficiency of xylose, you get 0.08 kg (0.10 l) of ethanol, 0.15 kg of CO2 emission, and 0.08 kg of other mass.
The balance is 0.27 kg of lignin, at 21 MJ/kg energy content, or 5.7 MJ. Biorefinery direct energy requirement for cellulosic ethanol production is 28 MJ/l-output (EBAMM 1.1), or 8.2 MJ to produce the 0.30 liters from the 1 kg of switchgrass input.
My question is, how does this 5.7 MJ of lignin per kg of switchgrass input provide all the processing energy in the plant (including drying the lignin, which is in solution when separated) and generate enough electricity to export 1.9 - 5.4 MJ/l of electricity? (Range in Hammerschlag)
If you zero out the lignin "credit" in the biorefinery in the EBAMM model, the EROI drops to 0.88, including the 4.8 MJ/l "credit" for some undefined byproduct.
Anaerobic digesters use wet biomass to generate methane which can then be used by the biorefinery instead of natural gas(fossil methane). An Iowa engineer figured that a distillery's entire energy needs can be met by digesting the cellulose and lignin portions of the corn kernels.