sorry- sometimes i erroneously assume that everyone's going to know what i'm dealing with here, because i mostly post about my cb550F with the 718cc engine i've built for it. the switches are from different year cb550s, and the alternator portion will be from a '76 cb550F. i chose the 500 harness, because i had one, and i really just wanted the proper colored wires to work with. i just wired everything up, and taped and connected everything well, but the harness is essentially like this:
battery + --->split to rectifier and main fuse.
battery - --->connected to frame, green wire circuit, and black sire from the dyna 2000.
main fuse---> to switch (toggle), which powers the black wires.
black (switched) wire powers ignition circuit directly (fused at 15A)
5A fuse between black wire junction and brown/red, which powers the headlight
5A fuse between black wire junction and brown and green/y, which powers the taillight and brake switches.
5A fuse between the black wire junction and the grey wire, which powers the turn signals.
the entire alternator circuit will be connected as per stock diagram, but is currently not in the picture at all, except for the regulator which is connected to the black circuit, green circuit, and the white wire which is going nowhere for now.
everything has a clear return path to the battery through the green wires, as well as being grounded through the frame. the engine is grounded to the frame, at the same point as the rest of the green wires to guarantee a good ground for the spark plugs.
my harness has one fuse more than the 550, and three more than the 500- all blade fuses. nothing is blowing, nor are any wires heating up. it's the (green wrapped) winding on the outside of the regulator that is heating up. the thing is, in the stock location i don't think i ever really touched it, but i moved all my electrical under the seat and now i did. too bad TT is boycotting my threads... i bet he'd have some good advice.

by the way, this link did wonders for my understanding of wiring (and a physics tutorial on electricity i read recently about tube amp repair):
http://www.gabma.us/elec/proper_grounding.pdf