Measure the current between the rectifier and the batteries. Multiply by the charging voltage. (Of course current is probably what you're really interested in anyhow, since it represents amount of charging.)
You can use a section of one of the wires from the rectifier to the batteries as a shunt, by soldering finer wires to it at two points, hooking the other ends of the wires to a digital multimeter set on a millivolt scale.
Consult a wire table to pick a distance between the two probe taps that corresponds to some nice power-of-ten fraction of an ohm. For instance: With 0.001 ohm of shunt one milivolt on the meter means one amp in the wire.
Fine tune the calibration by putting both the shunt and a good reference ammeter in series with a battery and a decent load (like something drawing 10 or 20 amps) and fine-tune the location of one of the taps until the meter readings correspond. (Be sure to let the wire cool for a couple minutes, or quench it with room-temp water, after using your soldering iron/torch to slide the tap to the new location). Use lots of solder and flux. (It doesn't appreciably affect the resistance and thus the desired shunt location, since copper is so much more conductive - and you're tuning for the right reading with the total copper-and-solder system anyhow.)
If the wire you're using as a shunt is stranded you want at least one of your taps to be wrapped and soldered all the way around it, so the resistance between the strands doesn't foul up your readings.
DON'T try to put your sense wires on a connector with the shunt, or in a connector crimp with it. You don't want the connector resistance to foul your readings. Start with a continuous section of nice, fresh, wire and put your taps on it - then (when you're done tuning) cover it with insulation or "liquid electrical tape" to protect it from oxidation.
You can make your homebrew shunt near one end of a piece of wire with extra length and then cut it to size (as long as you don't screw around with the section between the taps or really close to them). Don't flex the section between the taps any more than necessary when installing it - though you can flex the sense lines all you want.
