In my experience most distributor based systems have the timing defined by mechanical or electronic points within the distributor. Where these are used with electronic fuel injection, there is typically a signal from the distributor to the ECU to trigger the injection. Are you certain that in your case the timing goes the other way? Where does the ECU get its crank position information from in this case - do you have a separate crank position sensor?
Assuming it works as you describe, what the distributor sees from the ECU would be a sequence of pulses (one per spark event) with no indication of which one was associated with which cylinder. Your ignition router need to know either the crank phase or the cam phase to know which cylinder to route this spark event to.
Quite likely you could get away with a wasted spark setup, in which case you would fire the coils in pairs. With this arrangement you would need a crank phase sensor. If you already have a trigger wheel providing a crank position signal to the ECU, it would be tempting to try to use the same sensor but I don't think that will work unless you are clever enough to design some clever electronics to sense the signal without attenuating it. If you can install a second MVR sensor on the same trigger wheel that would do for your ignition router, but whether that is practical would depend on your engine design.
If you can't / don't want to use wasted spark then you would need a cam phase sensor instead. In the past I've made one of these from an ordinary dizzy by removing all but one tooth from the rotor that triggers the points. Other people have attached an MVR sensor to the rocker cover and picked up movement of a rocker arm, or overhead cam drive pulley.
If you can solve the problem of working out which cylinder is associated with which spark, the rest of it seems feasible. (I'm not convinced that this would provide any significant benefit over a distributor-based system if you're retaining the original ECU, but that's your affair.)