I don't have any answer here, but am sure there is a limit to the extent draft animals could be used. Biogas is one. Methane can be made from manure, and the residue left over is still good fertilizer. It can also be made from garbage. All our landfills should be producing methane.
Ethanol is another.
In Brazil ethanol is made from sugar cane and in the U.S. it is made from corn. Also, counting all the energy to grow the crop and produce the ethanol, there is more energy put in than you get out. A better system would be to make ethanol from wastes or perennial crops grown on marginal land. The practicality of this has not yet been demonstrated, but it holds promise. The ultimate source of sustainable energy for agriculture, as well many other uses, is solar generated hydrogen.