1) How are you measuring the rectifier? Your description is not too clear. Most digital mutimeters have a "diode test" function that displays the voltage drop across a diode junction - should be around 0.5V "forward" and an indication of open circuit connected "reverse" - display varies, could be "ERR" ... whatever it displays with the leads not touching anything. There should be open circuit between all yellow wires, both directions. All 3 yellow wires should show ~0.5V when connected one way to the red wire, and open circuit the other way. Same with all 3 wires measured to green or ground, but reversed from the readings to the red wire. If you don't have the diode test function, reading resistance is similar but the forward reading will be some low Ohms number and reverse very high (or whatever it says with the meter leads loose). Analog Ohmmeter the same, low reading forward and high reverse.
2) Adjusting the regulator is usually a mistake: it's pretty simple and the settings don't tend to change on their own... until you have resolved any harness and switch issues you're just pissing into the wind by adjusting it. The regulator measures system voltage and connects power to the field coil when it decides the voltage is low. The trick is that the voltage it measures needs to be accurate, and a harness with corroded connections and switches won't provide an accurate voltage - you get a voltage drop proportional to the current draw. If the voltage is a bit low you get overcharging and the battery "boils" dry... not your problem. If it's really low there isn't enough there to drive the field coil properly and you get low alternator output.
3) The alternator is really very simple. You need current through the field coil (white wires), with the rotor turning it generates 3 phase AC electricity between the yellow wires, converted to DC by the rectifier. Output power is directly proportional to field current and somewhat proportional to rotor RPM... reduced a lot at low RPM but not increasing much above 3000 or so. All the connectors in the white and yellow wires need to be clean and tight. That's the engine plug and the various bullet connectors. The bullets under the sprocket cover get heat cycled with the engine and tend to get corroded before any others.
3) A simple test is to connect the white and black wires to the regulator together - the spade females can be pushed together to make a decent connection temporarily as long as the joint doesn't touch the frame or anything metal, or use a jumper wire between the regulator terminals. That puts the alternator at 100% power: with a fully charged battery its voltage should go above 15V at 3000+ RPM. If that works but you still don't have proper voltage with the regulator reconnected, then a new regulator or some adjustment of yours is in order. The regulator should - with lighting loads off (HEAD and TAIL fuses removed) - settle at around 14.5V at the battery with the engine above 3000 RPM. Note these tests absolutely require a fully charged, known good battery. Use the kickstarter for the tests, the starter motor discharges the battery a fair bit even when used only for a second or two.
Going through the harness and cleaning the connectors - at least all the red and black wire connections - plus switching the key and kill switches many times to rub clean their contacts will solve many electrical problems.
