... when I check the voltage on the wires running to the bus lights, they are only 9 volts, doesn't matter if it's markers, blinkers, breaks, etc, it's all 9 volts. To eliminate a ground issue, we run a wire directly to negative terminal of the battery to the ground at the lights, still only 9 volts, we then ran a wire directly from positive side of battery to the lights and got the full 12.5 volts, and the lights got a lot brighter. This means somewhere between the battery and my tail lights, I'm loosing voltage.
Corroded terminals and/or wire somewhere between battery and lights. Could be bad contacts in a relay. Could be a bad breaker. Could be the switch.
You'll need to figure out where the feed wire is connected to the battery, and where it goes. Start at the beginning and check the voltage at every
junction along the way. Could be the main battery cable is corroded right at the battery terminal. Not uncommon. Could be corrosion in a wiring panel.
Also not uncommon as many were installed in the engine compartment where there's persistent road spray from the tires and radiator fans.