I finally was able to use the machine to autonomously print a series of jobs. 

I manually stitched together the G-code of different 3D parts as one file. Before the printer starts a new print, the print head homes itself by hitting all of the end stops. This turns the conveyor motor on and ejects the previous part.

[Figure 1: Autonomously Printing Series of Parts]

I uploaded the collated file to the 3D printer and successfully printed a series of parts.

Two things should be improved with the system. 

1. A person should be able to print a series of jobs without manually stitching the G-code files together. There should be some software application that allows users to make a queue of files to print. The software application should allow users to still edit/add/delete files from the queue after the queue has been sent to the printer.
2. The G-code should be optimized for mass production printing. Right now the G-code forces the printer to cool down after every part is finished and then reheat for the next job. This drastically increases the total print time.