The two pin blue connector is used for the Alarm when fitted. It has a locking tab, so it clips on to the headstock group of connectors. It sits in the middle bottom, with the big 12 way on top.
On my bike looking forward from left to right the connectors are:
Black 6 way. ------------12 way. -------------- Grey 8 way
Orange 8 way.---------Blue 2 way.------------ White( translucent) 12 way
The single connector with the green wire might be for the old Denso Generator (Alternator) but I'm not sure. I take it your alternator is a Bosch, so it uses a different circuit.
However, You will find that the green wire will be powered when ignition is on so make sure the connector is stowed safely.
On my bike looking forward from left to right the connectors are:
Black 6 way. ------------12 way. -------------- Grey 8 way
Orange 8 way.---------Blue 2 way.------------ White( translucent) 12 way
The single connector with the green wire might be for the old Denso Generator (Alternator) but I'm not sure. I take it your alternator is a Bosch, so it uses a different circuit.
However, You will find that the green wire will be powered when ignition is on so make sure the connector is stowed safely.

)I will try your way first.
. Anyway it's a lovely fit now.
I will send it now.