The bike has simple engine management system. A Wasted Spark. What this means as Matt (Mouthfulloflake) has explained, is the hall sensor controls the timing for the spark and the fuel injector. What you need to know, is that on one rotation of the engine. Both the left and right sparkplugs fire at the same time. Also both the left and right injectors open at the same time. When this happens only the cylinder in compression will go bang.
My money is on the HES. However, because you or somebody has been fiddling with the motronic, which is normally extremely reliable, all bets are off.
You could try this:-
Take the right spark plug out and connect it to the stick coil and make sure the plug is grounded.
Take the left injector out and place it in a suitable clear container. Try and seal the injector in the container for added safety.
Ignition on and Turn the bike over. A serviceable HES will give a spark on the right plug and open the left injector. The fuel pump will also be heard running.
To eliminate the unlikely possibility that you may have failed stick coils, then you could try this procedure using the lower secondary plug.
However, even this check will not be conclusive, if you have a faulty HES, and not a completely dead HES, then as you have experienced, it is possible, though with some difficulty to get the bike to run.
Ian