The rightmost breadboard was replaced and all of the components were replaced into another breadboard. The encoder section of the circuit (leftmost breadboard) had 10k resistors removed and the signals from the encoder had more fidelity. The encoder signals were routed to the 74LS00 (which acts as an isolation to the MCU and an inversion) and the output of those are connected to the Atmega328P. The Code was then updated and we have a visible reading from the seven segment displays. But not everything is working. The Segment displays do not output a live reading from the enocder very well.