My thought is to delay the power down of the ecu when the ignition +ve is dropped, may be use an input for the ignition sense, this then also powers the ECU in parallel with the main relay switched power source. The main relay controled by the ecu as per normal but is an off delay latching circuit. so when the ignition sense input is dropped, The ignition and fuel is stopped, the off delay is started, the ecu still powered via the main relay switched power source untill the off delay has expired, then the latching circuit is broken, thus dropping all power from the ecu.
Work into this as the of delay is counting down, the stepper motor positioning to say maybe the last PID bin value of 40 steps, for example, obviously the stepper needs to close fully first to ensure it knew it was at zero steps, but it would then open to the 40 position. So, when the engine is turned on the stepper is at a 'known' 40 steps it just has to open to the cold steps position as per coolat temp PID bin value and steps when starting scale. Response is far quicker an prevents anyone trying to start an engine on a shut throttle, even if it is only for a couple of seconds.
Obviously there are still more pressing issues to be resolved with the stepper control such as the stepper closing the throttle completely on overrun. I can see the above being achieveble if one of the misc outputs had an off delay, much like the fuel pump. The output in question would need to be linked to the input used for sensing the ignition switch as well.
This theory could equaly apply to electric water pumps to run on for a time or until the engine temp is below a set limit to prevent major heat soak.
