Brown/yellow is the wire to the dash lamp, which does connect at the regulator but doesn't go "through" it. I'm not sure which alternator you are getting from Moss, but if it needs the brown/yellow, then you can either splice the two NY wires together near the old regulator connector; or just leave the connector in place and insulate it somehow (so the terminals can't touch ground).
Both the factory diagram and Dan Master's diagram show a brown/green (NG) and a brown/red (NR) to the regulator; however it may be that the factory actually used a brown/white instead of the brown/red. The NR is supposed to connect to the hot terminal at the solenoid, while the NG supplied field current to the original alternator. If your new alternator needs a "sense" connection, then one approach would be to splice the NG together with the NR (or NW), and use that for the "sense" connection. If not, then they can be removed or tied off and abandoned.