I was excited as this is a topic I plan on researching more (especially a few weeks after apple season), but there was some sort of preventative measure in place so I was unable to read/see anything.

The book "Alcohol Can be a Gas" has pretty much all you need to know about making alcohol. Its not that expensive either, for its size and detail. It is 640 pages.

I am curious about making a foodstuffs based fuels like ethanol, especially when looking at issues like desertification, the diminishment of the aquifer of the Great Plains and the drying up of many rivers.  If we use a host of genetically engineered crops to convert soil nutrients and water into fuel to burn in our cars to get around, will we be wasting two far more important resources?

no foodstuff crops can compete with the other available feedstocks, like mesquite beans (drought tolerant, nitrogen fixers, produce as much as corn per acre), prickly pears (dourght tolerant, good food for animals, produces 2-3 times what corn does per acre), cattails (wetlands, produces 10X what corn does per acre, considered a weed), and don't forget about fallen/damaged fruit....

All of these feedstocks could be grown on marginal land that isn't needed for food production.  Combine that with permaculture techniques, and you have ethanol without fertilizers, without irrigation, growing on marginal land, and can out-compete corn ethanol.

There are lots of desert plants that are suited to starch/sugar production, and nearly every single one of them produces 2-3 times or more the amount corn does per acre.