I had a problem with the battery getting lower than normal charging voltage on my 1998 LC. Electrical checks on the regulator/rectifier (RR), the alternator, and battery showed that they were working ok. The problem turned out to be excessive voltage drop from the RR to the battery while under load. The stock RR connection on my bike to the electrical system is at the far end of the main wiring harness from the battery. As with any electrical system there is some resistance. The total resistance in my wiring harness including the connectors is small enough that it won’t register on the average VOM. However, when passing large currents the resistance was enough that it reduced the effective charging voltage to the battery.

I connected a separate positive lead from the RR to nearer the battery so that it bypassed any resistance that may be in the wiring harness. The battery now "sees" the RR output directly. My charging voltage at the battery increased to 13.75 volts in the cruise rpm range using the stock RR. This is after riding at highway speed for a few minutes to let the battery charge and the system stabilize, and with driving lights on. The voltage increase doesn’t seem like much but it is a lot in the charging world.
 

I also tested an aftermarket RR, which showed a slight performance gain over the stock unit in the cruise rpm range; voltage at the battery measured up to 13.95 volts at cruise. Note that the performance difference between my stock RR and the aftermarket unit may not be universal and may just be particular to my units. Also, the voltage output of both units varies with rpm, generally decreasing somewhat at speeds above 2000 rpm or so. I think this may be characteristic of permanent magnet alternators and the type RR that most motorcycles have. The solid-state components in an RR may not be able to keep up as well at the higher rpm/frequencies.

Wiring:
Note: The descriptions below are for my vintage ’98 LC. Some of the wiring may be different on later model bikes.

I made the new connections (two) with a separate 12-guage wire. One end of the wire is spliced into the red positive wire at the harness RR plug, and the other end is spliced into the red main positive lead at the outlet of the starter relay.

Sometimes I use good crimp type connectors. I do a bit of testing and it’s easy to remove the connectors when I want to make changes. Soldering is a more positive method for high current permanent connections.

Doing it:
Disconnect battery negative cable. Remove left side fake tank cover to get at the starter relay area. Remove secondary gear case cover. The RR is bolted to inside of cover. Unplug RR and set cover aside.

I routed the new wire from starter relay area along upper frame rail and down to RR plug. If following existing wire harness, remove seat. The wire can carry significant current. Use 12-gage wire. I used extra sheathing all along the route for added protection and to ensure wire will not rub through.

RR connection: On the bike harness RR plug, there are five wires. The red wire is the positive wire connecting the RR to the electrical system. Splice new wire to red wire.

Starter Relay area connection: Remove clear plastic cover off the starter relay. There are two heavy wires connected to the left side of the relay. The red is from the battery, and the black goes to the starter when the relay coil is energized. There is a smaller red wire on the right side of relay coming out of the top. There is also a 30 amp fuse plugged into the top of the relay. Power comes from the battery feed into the relay body, through the fuse, and then to the red wire on top of the relay to the bike electrical system. The other wires coming out of the top of the relay are for activation of the starter relay coil.

Splice new wire to the red wire that comes out of the top of the relay downstream of the main 30 amp fuse. This keeps the main fuse in the system between the battery and the splice. For better access, I separated the bundle wrap farther on up and made the connection a little away from the starter relay.

A fellow LC’er has a nice web site with some good pictures of the starter relay area. (He also has some instructions on how to rewire the main feed from the battery so that it bypasses the starter relay using an external fuse). http://www.crowitis.com/wes/electric1.html