Now I can record the serial stream into the data logger and analyse what's going on. I used the info to make up a software 'dummy ECU' to feed made up data into the programming software and work out what the remaining data channels were. This is how someone did it with an aftermarket car ECU.
It might need some tinkering with baud rates, parity etc to get the settings right but when you hit the sweet spot some pattern of data should become apparent. If the ECU streams data out, so the programmer can see what's happening with sensors etc whilst the engine is running, then it should be feasible to connect the serial line to something like Hyperterminal or Portmon on a PC and watch the bits arrive. It probably uses a serial signal for the programmer to ECU comms. So there's more on that line that just a voltage to blink the fault light. The workshop manual says the Yamaha FI programmer plugs into the 'self diagnosis connector' in the yellow/blue wire that connects to the dash.
