You may have already done some of this, but assuming you have'nt, I'd start with back tracking and checking the wiring connectors to the ECU.
Then remove the coil from the plug (leave the coil connected to the wiring harness, as well as leave the sparkplug in the head) and stick another sparkplug in the coil, ground the sparkplug somewhere on the engine (don't hold the coil....I believe theres exposed metal on the sides?) Fire up the bike and see if it's sparking.
If it is I would assume the fuel injector is not working/getting fuel? The manual works from the small to big of: connections, shorts, open circuits, component failure, and the last resort being to contact MZ...which probably means the ECU is afoul. That's assuming the diagnostic tool is being used. Everything is a just guessing game otherwise....have you disconnected the battery for a few minutes and reconnected. On some vehicles that is required to reset the computer. Again, just another guess. That's all I've got. Good luck!