Hi, most of what you are suggesting has already been done, by the likes of WRAP, see: http://www.wrap.org.uk/sites/files/wrap/The effects of AD on common crop pests diseases.pdf The issue of un-digested material and retention time is a subject that can be complex, as it has many influences such as regulations, type of feed-stock, gate-fee's etc. However as a general rule of thumb a reasonably well designed and operated plant will ' wash through ' around 1-1.5% of the feed-stock un-digested as each batch is fed. This material can cause a problem if stored in sealed tanks, or covered lagoons. in hot weather. In general it is not to much of an issue, and in some cases as described by sjt01 above, it can be recirculated again through the process. The basic design criteria for retention time is that it should not exceed the life of the longest living bacteria. These vary with temperature, so higher operating temps require less retention time than lower temps.