ok, im not sure of what you're even doing here, for one why do you have 4 wires comming from your stator going to the diodes? don't use the center wye. also check that you did hook the diodes like in the schematic.
now you have a dc output. what you need to do next is get rid of the water cell, you need to determain your polarity.
take the 2 leads comming from your rotor, now take the 2 leads comming from your diodes. Connect the leads from the rotor to the leads from your diode, Did you notice anything? if NO then switch the wires and try again.
when you notice a spark when doing this you should note what wires was connected to what when you got this spark, this will be your setup. the rotor can only hook to the stator 1 way, its up to you to find it. you may have to hold the wires together for a short periode of time, "until votage starts to take over".
if you failed with the instructions i have given you above then do it again, but this time hook 12 volt battery to your ROTOR for about 6 seconds, this will train or condition the rotor. when you have your rotor conditioned never hook it up backwards to a battery. Then repeat the steps above.
after you have confirmed that you can get sparks from the alternator setup you should have noted how all the wires go together. when you get this information then you add a mosfet "between the wire comming from the rotor where it is connected to the stator", then you regulate it with the circuit we have provided.
when you get all this connected then hook your fuel cell up.
restart the process, "Amp meters between the Rotor and Stator has been known to kill the process."
now if you have a failure, bump the 12 volt battery to the rotor, "with your setup in tact and your pwm circuit off", hold the battery to for 3 seconds. remove the battery and power on your circuit, power it up and hope for the best.
the mosfet is touchy as well, there is a certain way, way you can install the mosfet between the stator and rotor, and i forget wich lead to connect it to.
the circuit you're looking at is the ideal, it has not been confirmed that it is the exzact way everything should be connected.
bee looking for your reply on the next test you run.