This paper presents a system to control Autonomously Guided Vehicles (AGVs) in a flexible manufacturing setting allowing numerous vehicles to make informed decisions amongst themselves as well as between the governing computer system(s). These decisions allow work order acceptance, path planning, navigation, and traffic management to be autonomously operated - rather than pre-programmed as are the traditional methods. This paper is mostly focused on the work order acceptance protocols, as this is the area which is of most benefit to a flexible manufacturing system. Some work on autonomous path planning is also involved, but since a guided system is still being used, this logic is limited to pre-set paths only. Such autonomy of the entire system would benefit a manufacturing setting by allowing the vehicles to be flexible in their work and ready upon command for whatever job the user requests. The vehicles are modeled using the Lego NXT Mindstorm kits to demonstrate the functionality of the communication protocols created through this paper.