I think nitric acid is going to be a very helpful waste product to collect. It can be used to precipitate products from basic solutions, or to break down organic matter for easier digestion by bacteria/yeast/fungus (saccharification of cellulose). Its salts are nitrogen salts that are used as fertilizer.
Even if there is a period where no acid is needed for anything, using urine to neutralize nitric acid gives ammonium nitrate. Sometimes used as an explosive, i suspect that saturating ethanol or methanol with it (as alcohols are polar and could slightly dissolve salts) would increase the energy content of the liquid fuel. The urea in urine (its main nitrogen containing compound) will break down into ammonia in acidic solution and thus much of the nitrogen in urine could be converted into fertilizer/fuel.