Glad Manfred has you sorted..... Spark plug tip that goes into the coil can vary depending on the coil. Stock MV Agusta coils require the "bulb", screwed on cap.
Other brands of coils may require just the threaded post. I do not know what the Fiat coils require, but obviously you have figured it out.
I am not sure your bike has the coils firing in pairs.... That is found on the earlier models that used the Marelli 1.6M ECU. It also fires the fuel injectors in pairs.
I believe your bike has the 5SM ECU which fires coils individually (and injectors). Does your ECU have 2 large wiring plugs or a single plug?
That's the 5SM...fires ignition and injection sequentially one at a time.
Workshop manuals usually cover more than one model...always make sure you are looking at the correct electrical system in the manuals.
Anyway, sounds like the spark plug to coil connection was your problem. Happy that was an easy fix.
This is the tool I use for throttle synch...a bit less costly than teh electronic ones and works just fine: