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It sounds like you have a charging problem or your battery is shot. Check your belts and your battery, if they're both good be sure all your grounds and battery connections are good (no corosion or loose connections- especially the ground points at the engine.) If you're still having problems you could need a new alternator or voltage regulator.
The voltage regulator it in the ECM.What you need to do is go to the basic which can be overlooked like is the Alternator fuse burnt open that will require a new fuse, how is the battery terminal connection? You need to check that,Or how is the calbe from the alternator to the Battery is the connection in good shape? Those you need to check you mainly need a voltmeter to do this but a good visual inspection can get results,
Interesting. You may need a wiring diagram for the engine. Unplugging the regulator turns off the alternator which should not affect the ignition system. Unless it is over charging somehow. Or the alternator load on the engine is causing a missfire to be worse. Its possible you have a ground problem somewhere too.
There is a fuse under the dash that is the same one that operates the fuel gauge, if it blows the alternator wont charge. If the fuses are good I would take the alternator off and get it tested. Hopefully the rebuilder will warranty it. I would also make sure the new regulator is compatible with the old type regulator system. Most large auto parts stores can test alternators, and they normally do it free.
The stator only has two wires if it's an original stator. The pigtail from the stator has two wires inserted into a round plug, The regulator has three wires. There should be two short wires and one long wire. Or , two smaller wires and one larger wire. The two shorter, smaller wires go to the stator, The longer, larger wire goes to the battery from the regulator.
If your stator has three wires coming out of the engine case, it is probably a 3-phase stator which is available aftermarket. It take a special voltage regulator for this type of stator. That voltage regulator will have four wires coming from it.
corroded, burned, loose connection from the stator to the regulator (likely);
faulty stator (least likely).
The stator would be producing relatively high AC voltage while revving the bike. The stator output AC voltage are fed to the rectifier / regulator through 3 white wires. Check calls for testiing for the presence of the AC voltage on any pairing of the white wires before and after the connector before the voltage regulator. Check on the regulator calls for checking the battery voltage when revving the bike (14.5 VDC).
First, take your battery somewhere and have it load tested. Fat Boys are tough on batteries as the battery sits in the "horseshoe" oil tank and is subjected to high temperatures due to the hot oil in the tank. Battery life is typically two years although I've seen some go longer and some not last that long. Have the battery tested before you start spending money.
To check the stator, you unplug the regulator at the engine case. Down inside the plug you'll see some electrical connectors. Connect a DVOM (digital volt ohm meter) to these connectors (one lead to eac pin) and put the meter in the 50 volt or higher range AC voltage. This is important that your meter be set to measure AC voltage because at this point, the voltage is indeed an Alternating Current voltage coming out of your alternator. Start the engine and bring it to a high idle. You should be reading over 20 volts AC. The book says that you should read 12-18 volts per 1000 engine RPM. If your engine is turning 2000 rpm, your meter should read 24-36 volts AC.
To test the regulator, first charge your battery to a full charge. Then connect your DVOM across the battery, red to positive, black to negative. Put the meter in the 20 volt DC range. Start the bike and bring it to a high idle. The voltage will start at somewhere around 12.5 volts and climb to about 14.5-15 volts. This would indicate that the regulator MAY be alright.
Now, have you changed any of the lights on your Fat Boy? I've seen people change and add lights to the point where their alternator could no longer put out the current necessary to handle the load. If this is the case, you may need a higher out charging system.
I don't know where you're located but $260 seems quite high for a voltage regulator.
well what you need to do is take volt meter and start the bike see if you are getting 13,5 volts at battery or more if not hold throttle at 1500 rpm and see what you have if you do not have this volts coming to battery it could voltage regulator or stator is bad but check all grounds to bike and wiring hope this helps