Early lignocellulosic biorefineries have been plagued with many issues that involve feedstock handling problems and variations in conversion efficacy that stem from feedstock variability and complexity in dimensional, physical, chemical, and mechanical attributes. Feedstock ash and moisture content vary considerably in corn stover harvested from farms for bioconversion, and their effects on preprocessing (grinding/milling) and subsequent chemical and enzymatic conversion to fermentable sugars is systematically explored here using pilot-scale hammer mill grinders and chemical hydrolysis reactoris systematically explored. Corn stover with high ash content due to contamination from soil was found to (1) consume higher power during grinding and resulted in reductions of processing rates, and (2) produce a larger fraction of fines in the feedstock that were lost to dust mitigation systems and caused higher mechanical wear rates. Corn stover feedstock coming from fields with a high residual moisture content resulting in bale degradation due to self-heating caused a more pronounced drop in preprocessing throughput due to grinder overloads and process upsets leading to equipment downtime. Conversion yield to sugars was not affected, although differences in fermentation performance on these sugar streams was not examined. The overall process throughput was only 40-70% of nameplate capacity due to preprocessing problems.