You have identified them correctly.
The additional instruments plug is for optional extras, for example a fuel gauge. If the bike was sold without optional extras, then nothing will be connected to it, unless other modifications were made later.
A lot of the wires come from the relay box, but two come from underneath, one from the hall sensors, and one from the oil pressure sensor. There is a hole in the plastic base near the coolant filler cap. If only the hall sensor wiring can be seen, the oil pressure wire may have fallen under. It looks like the base has been removed, but originally it came up from the right hand side, near the filler cap.
