Was the stator and rectifier replaced with new or used ones?
Start by checking the AC output of the alternator. Check between the yellow and pink wires coming out of the engine at appx. 2000rpm - the voltage should be about 28 to 40 volts. Higher is OK - below 25 is bad. It is possible for the rotor to be bad, but it is rare.
If the AC voltage is good, check the DC voltage across the battery (with a fully charged proper battery TX9-BS) (the battery might be a YTX, BTX, CTX or other prefix depending on the brand) - a fully charged battery has about 13.2 to 13.8 volts
DC voltage across the battery needs to be about 14.6 at about 2000rpm
If the voltage is above 14.8 or seems to fluctuate, switch your meter to AC - if the reading steadys out and is high, that means your rectifier is shorted out and AC voltage is going to the battery - AC will kill a battery
If the tests seem ok, recheck the grounds from the battery to the frame, battery to engine, wiring harness to frame & voltage regulator to wiring harness.
The charging system on the 400EX is about as simple as they get. Single phase alternator, full wave rectifier and wires.
Good luck - a full test is detailed in the service manual, but if these check out, the previous problem was probably just a bad battery. Remember - the charging system is designed to maintain the charge on the battery - trying to charge a battery with the vehicle's charging system usually results in premature battery failure or damaging the charging system
