I wanted to create my own thread on this topic, as the method that I've come up with overcomes several of the disadvantages of other methods. I feel that I have a lot of information out on twitter and in other threads, but it would be nice to consolidate it all into one thread that can be updated as I test.
The concept for how this test works is to watermark the screen image at the exact time the controller is being pressed. This is done using optocouplers, so that there can be no electrical cross talk between different components of the testing circuit. This should ensure mean that the signal arrives at the controller at the same time as it interrupts the video signal.