The success of the bioenergy sector depends significantly on ensuring efficient and sustainable biomass feedstock production and provision, which requires a comprehensive systems theory based approach. BioFeed is a system level model that has been proposed to optimize the feedstock production and provision activities, and has been applied in the past to study switchgrass production in Illinois. This work presents recent additions to the BioFeed model to enable a more accurate representation of various biomass production activities for the energy crops. While maintaining the original model framework that focused on farm level design and operational issues in addition to storage and transportation logistics, new biomass packing and size reduction operations such as peptization and grinding have been added. The selection and operation of biomass handling equipment such as loaders, unloaders and infield transportation equipment have also been incorporated. The addition of these new operations creates the challenge of ensuring the logical validity of the operational sequence during model simulation. A super-structure of all possible operational sequences is developed and the biomass form at the output of every equipment is tracked to ensure appropriate equipment selection. The model is then applied to a case study of Miscanthus production as the energy crop in southern Illinois. The results show that the optimized delivered cost based on existing technology is about 45 \$/Mg. Biomass packing and storage are important components of the total cost distribution. The potential alternatives to reduce the delivered cost include using a single-pass mowing and baling operation, increasing the packing throughput capacity, and extending the harvesting window.