Re :- connecting the alternator.
The blue and yellow output wires from the GTR alternator connect to any 2 of the 3 yellow wires on your Honda reg/rec unit.
The third, brown, output wire from the GTR alternator is only switched in when the lights are turned on, supplying additional power. It does this via the white wire which runs from the ignition switch back to the rectifier. So the third yellow wire on the Honda unit is connected to the white wire, not the brown. Hope this makes sense.
Brian.