Yesterday I helped someone troubleshoot a problem with their new CP3 setup and I had to come up with a set of tests they could run with what they had on hand.
A Dual CP3 controller should just supply the second controller with the same signal as the first controller so all you need is a way to backprobe the two CP3 connectors and two identical test lights. It would probably also help to have long wires so you can bring the test lights into the cab if necessary.
Start by connecting to the FCA on the second CP3 pump with one of the test lamps. Turn on the key and start the engine. The light should turn on almost fully. Rev the engine a bit and as the ECM commands more rail pressure, you should see the light dim slightly.
If the light does not light at all, first make sure the light works, then make sure that the light is actually connected to the pins, make sure the controller cable to the first CP3 is plugged in properly and lastly make sure the 12V supply and the ground connection to the controller is good. If all that is true, then the controller is most likely bad.
If that test passes, you may now hook the second test light to the stock CP3 connector. Starting the engine should now make both test lights light up. This is where long cables on the test lights to allow them to reach onto the cab will be useful. Drive the truck and the light's brightness should track reasonably well. If the lights are not identical the brightness might track differently, but they should get bright and dim together. If they get bright and dim together, then most likely the CP3 controller is good.
Sometimes you just want to test the pumps, the easiest way to do that is to take them out of the circuit one at a time. For this you'll need the connector that plugs into the CP3/FCA with wites long enough to connect to the battery. Supplying 12V to the CP3 will ask it to provide the least amount of fuel possible. The truck should run the same with either pump out of the circuit. Though if one pump is stock and one is modified, you might find that one makes a bit more power than the other
Ira