As most owners are aware, the charging circuits of the Pegasos have a propensity to develop problems. One of the most common problems is the Regulator putting out too high of a charging voltage, which will cook the battery over time. As an electronic engineer at work, and an owner of a '98 Honda VFR800Fi (well known to develop similar problems) I had a pretty good shot at being able to suss out what was going on.
The stock R/R on the Cubes is the SH532B-12, which is a 6 wire R/R. Though people often blame this unit for being too wimpy, it is a very common model of R/R found on motorcycles of many other brands, for what it's worth. The three yellow wires are the 3 phase AC coming from the Alternator stator windings. The other three output wires are a Red/White + DC output wire, and a Brown - output (common) wire, and then there is a Green + voltage sense wire.
In the stock configuration the three yellow wires are connected to the three yellow/black wires from the generator's stator with small round molex type connectors. The brown common wire goes to a ring lug and it is bolted to the rear sub-frame where a blue ground wire also resides. It is actually the blue wire that gives us the return path to the battery and charging system common, not the frame contact. In fact the paint has not even been removed from under these lugs on my bike. The Red/White wire connects to a Red/Orange wire in the harness which goes through a 20 amp main fuse right to the battery positive side. And finally the Green R/R wire connects to a Green/Orange wire in the main harness that supplies a switched 12V from the ignition switch. The R/R adjusts it's output voltage based on what it senses for voltage on that green wire.
The problem is that during operation the current through the ignition switch contacts and all of the other distributed resistances of various connections, all of which will cause a small but finite amount of voltage drop at that sense wire, tells the regulator to produce more voltage at the main output wire. I have often seen 15.1 - 16.0 volts at the battery terminals because of the losses at that sense wire. This charging voltage is too high for the battery and will eventually cause damage to it over time. Since the primary objective of the R/R is to maintain the charge on the battery, the ideal regulator output is one that provides 13.5-14.2V to the battery at all times.
My Fix:
First I cut off all three of the little molex connections from the yellow stator wire connections and crimped on some male and female spade lugs to get more secure, lower resistance connections. Use adhesive type of quality shrink tubing to insulate, weatherproof, and mechanically support all connections.
Next I disconnected the red and green R/R wire connections and removed the spade lug type connectors from both sides of the nylon connector bodies. I taped up the old Green/Orange switched sense wire from the harness as that will not be used any more (but you may want to keep it handy to use that as a switched voltage source for something else in the future).
Then I connected the R/R's green sense wire to the Red/Orange wire (that used to be the output wire) which goes directly back to the battery + terminal through the 20A main fuse. So we will now be taking our V sense right from the battery instead of on the other side of the ignition switch.
Finally, I made a new (heavier, I used 10 gauge) positive Voltage output cable to run directly from the R/R's Red/White wire to the + battery terminal. You should be sure to have an inline fuse installed in that new wire to protect the battery from damage (and explosion) in the event of a shorted R/R.
Here's the diagram of the modified circuit compared to the stock wiring:
Stock
Modified
In the above diagrams 26 is the stator, 25 is the R/R and 24 is the battery
The results are exactly what I was looking for. After starting the bike the panel voltmeter I have connected to the battery shows the voltage slowly climb up from ~12.8V to 14.2 volts while on fast idle as it recharges, which is where it stays pretty much all of the time now except when the bike drops down to low idle. At that time, the alternator (stator) cannot keep up with the current demand and the battery voltage drops down to its nominal 12.8V. Left idling long enough it may actually still result in some battery discharge, but any operation above about 2000 rpm is enough to bring the charge voltage back up to 14v and recharge the battery.
Note: An even better method would be to run a new sense wire all the way back to the battery terminal to eliminate the small voltage drop on the 20A main fuse. But that error is pretty minimal, so I'll just live with it like this for a while now.