Usually we consider primary energy, i.e. 100% conversion efficiency. However, for realistic studies we need to consider the actual energy conversion efficiency.
Those who are involved in 2nd generation lignocellulosic biofuels do consider conversion efficiency quite a bit. This has been on going since the 1980's after the energy crisis. The technology has progressed. Many improvements in enzymes and other lignocellulose treatment processes have been made and continue to be made to increase conversion efficiency. See Iogen Corporation as an example of a leader in lignocellulose-based fuel production (http://www.iogen.ca/).
Thanks Jeffrey. But this website doesn't provide conversion efficiencies. It just provides over-all climate benefit data. I need values so that I could use them in my studies. Do you have any other source of data which I could use?
What is the scope of your efficiency that you are interested in? The GREET model by Argonne National Lab might be your best source of data (albeit a plethora of data) http://greet.es.anl.gov/
I might have some more insight if I know your exact scope? Are you considering the harvesting? Thermochemical conversion or only biochemical? Are you limiting yourself to a specific technology or fuel?
Say I harvest x kg of Miscanthus. Under my present assumptions, x kg of grass is converted to x kg of ethanol (fuel). This is not realistic. Due to conversion losses we could achieve x/y kg of ethanol. So I want to know this conversion efficiency of standard commercially available technologies (and source).
I would say that there are quite a few economics or technoeconomics reports on those answers because of the inherent intertwining of economics and yield. NREL has an extensive study on a dilute-acid pretreatment and biochemical conversion. It says their efficiency is 79.0 gallons per dry ton of corn stover. This is denatured ethanol, but a simple density translation can give you something closer to the units you'd like.
Personally, I feel your question doesn't have a precise answer. The conversion efficiency of biomass to biofuels greatly depends on the process you use and it's inherent conditions, as well as the type of feedstock you use. In the case of the latter, even differences in cultivars or varieties can have an influence on your final conversion efficiency. Moreover, even when conversion efficiency is high , this may not be the best indicator of the actual performance of your conversion system. Higher conversion efficiency may come at the cost of the overall economics and environmental performance of the industry.