I think I may know the problem, but it's hard to explain. There are three white wiring going to the regulator ( i think). I snipped all three so I could shorten them. I'm thinking when I put them back together I was careless and didn't connect them to the same wire they were originally connected to. I could undo it and go through all of the possible options, but that's a lot.
For some reason I figured since they were all white and all came to/went from the same place, it wouldn't matter. was I wrong? Looking at the wiring diagram I don't really see why it would matter, but I also don't get wiring diagrams super well.
Really should preview Drewpies Re-Wire clinic, posted on the XS400 home page, and under the Tech tab, on top this page. Anytime your re-joining wires that belong to the alternator circuit, you want to use Drewpies method of adding a little solder, to the connector.
Okay, the 3 white wires, come from the alternator, and goes to 2 different plastic connectors. then finally hits the rectifier. Our alternators are considered 3 phase alternators, each wire = 1 phase. The rectifier, has 5 wires, a ground, and a red or white wire (varies per model) . The Rectifier takes the alternators Alternating currents (A/C) and turns the energy to Direct Current (D/C) those diodes only lets energy pass one direction. Then in cooperation with the Voltage reg, it doesn't let the power get over the 14.5 volts. and fry out your battery.
So you are right.
The white wires do the same exact thing. so it doesn't matter. how ever, if your troubleshooting your alternator, you will need to get readings from each pair combination. so when you get there, let us know, or search, we have posted the answers.
by the way, I used this website to make sure I wasn't full of **it!
http://www.dansmc.com/electricaltesting.htm