Okay, some updates.
1: As you can see I got rid of the 12v to 5v converter because I located a 5v source at the ECM as mentioned above; pin #28 on the same connector the VSS wire uses.
2: Turns out it was pulsing too fast. I fixed this by throwing in an extra resistor. So now, in series between pins 6 and 7 there are a 10K Ohm resistor and a 47K Ohm resistor, which adds to 57k Ohms. (Previously there was just the 10K Ohm resistor.) I verified functionality by testing with an LED in series from the output to ground, so I knew that everything was working and that it would send the pulses to the ECM.
Okay, so on to testing. I had confusing results. In short, I don't know the correct inputs to make to get to autostop. Normally, when I drive, if I have my clutch switch off (driving the car in the normal fashion) and I hit the brakes, hold the brake down, throw it into neutral, then keep decelerating until I drop below about 35 km/h the car will autostop.
With this switch, I got autostop a couple times above 35km/h, but it wasn't consistent. I suspect that maybe the pulses I'm sending to the ECM are slightly too slow and maybe I need to remove the 10k resistor and just have the 47k resistor.
Also at some point I need to design a more ergonomic setup, right now it's still that thumb switch thing.