When the red wire is unhooked from the coil, there is no current flow in the circuit, so your meter is only measuring the battery voltage of 12 volts. Now when you connect the coil into the circuit, you have created a path for current to flow through the coil, through the Pamco (the pamco must be in the dwell period) to ground. The current flowing from the battery through the main fuse, the key switch, the ignition fuse and the kill switch creates something called a voltage drop. This is OHM's LAW. E =I X R . Voltage equals current times resistance. As an example the voltage drop is 3 volts (12 -9) , if the current is 4 amps and the resistance is 0.75 ohms, then the result is 3 = 4 X 0.75. That is why you see only 9 volts when current flows.
A more normal resistance for the fuses, key switch and kill switch would be about 0.25 ohms. Using E = I X R again, 1 = 4 X 0.25
In this more normal case, you would only have 1 volt drop, so you would have 12 volts from the battery and 11 volts at the coil/pamco.
So, somewhere along the path from the battery positive terminal to the ignition coil, your bike has a larger than normal resistance.
It could be a fuse holder/fuse or the key switch or the kill switch or maybe a combination of all of them. You need to measure the resistance of that total path, and then each device with an ohmmeter to see what you measure.
I'm going to suggest that the engine running rough has nothing to do with the Pamco ignition.
You could have carb problems or spark plug problems, etc. When was the last time that the engine ran with no roughness?
