Looking at the schematic, it shows the "state" of the machine when it is first powered on. The schematic shows the machine in tilt mode with the backglass lights turned on and the tilt light in the backbox turned on. The playfield lights would be turned off.
Here's a basic description of how power travels through the circuits in question:
When the machine is turned on, power exits the transformer, it goes through a 15 amp fuse, and then it goes through a bounce switch. The power continues traveling through the circuits and feeds power to various secondary circuits with open switches along the way, which are related to the score motor, score reels, reset relays, etc. The power keeps traveling through the circuit and it arrives at R relay switch (hold relay switch). This R relay switch is open and power stops at this switch. Power waits at this point till the R relay switch closes so it can continue traveling through the circuits. Beyond the R relay switch waits the O relay coil and the flipper switches. In order for power to arrive at the O relay coil and the flipper switches, the R relay switch must be closed so power can continue traveling through the circuits and various switches.
You've "isolated" the circuits by removing the the red/black wire from the 6th position ball count unit switch, which is the next switch in line from the R relay switch. So, in normal conditions, there is no way power can travel from the transformer side of the circuit. The circuit has been "cut."
So, if power is still getting to the O relay coil and the flipper switches, there is power entering the circuits "upstream" from the 6th position ball unit switch. With the red/black wire removed 6th position ball count unit switch, it creates a dead end. The next switch upstream in the circuit is the zero position ball count unit switch. Between the 6th position ball count unit switch and zero position ball count unit switch is a circuit branch that can send power to the O relay coil. When you manually opened the zero position ball count unit switch, power to the O relay coil was cut and the O relay coil turned off.
With these clues, it looks like there is a short in a circuit/switch upstream from the zero position ball count unit switch. Using the process of elimination method by checking the related circuits/switches, you'll be able to find the problem...