I can take a stab at your reg/rectifier..
For the rectifier portion, the Honda rectifier has the 3 yellow wires and the heavier green and red wires. It looks like these are the same for your new unit. The heavy red and green wires carry electrical energy back into the battery, with the diodes acting as one-way valves so power from the alternator can only go into the battery. The three yellow wires carry alternating current from the stator to the rectifier. Since the current alternates, the diodes sort out the positive and negative charges, so the order in which they are connected together doesn't matter.
For the regulator side of things, it's a bit different. The original Honda regulator has three wires, black, green and white. On your unit, the white wire would go to the white wire on the field coil, the black wire from the reg/rectifier would go to the green wire on the field coil, and the blue reg/rectifier wire connects to the black wire in the main harness.
I'll also show this "TwoTired" style...
Regulator/Rectifier unit Wire Harness
Yellow Yellow
Yellow Yellow
Yellow Yellow
Heavy Red Heavy Red
Heavy Green Heavy Green
White White
Black Green
Blue Black
Hope this helps!