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Your shogun does come equipped with a voltage regulator to protect your headlight, you shouldn't tap off the ignition circuit or directly off the alternator just for the reasons you listed, plus it can affect these systems unpredictably. Can you tap off the hot side of your horn before the switch, or taillight? If you tap off your headlight it would only work either in the high or low. Of course for the negative (-) side, grounding it any place on the frame is fine. Give these spots a try. Take care and enjoy your ride.
If the starter turns, but there is no battery power reaching the headlights and no battery power reaching the ignition system there is a fault in some part of the electrical system used by both headlights and the ignition system, but not the starter motor. Check all the fuses, if any are bad or dirty replace them then try again, then check the new fuses to see if they have 'blown' if they have you have a serious short-circuit in the wiring or other electrical component, replace the fuses again and remove all the headlight and tail bulbs and try again.
You have either a rectifier or charging coil(magneto) issue. The rectifier changes the AC pulse from the magneto to 12V DC. If that checks out, you'll need to test the magneto. Either case you'll need to have a multimeter handy and access to the factory repair manual for the testing parameters and wiring diagrams. Good luck!
well your magneto is fine(because your headlight works when you kick it over) I bet it is something as simple as you forgot to hook up a wire since you had it all taken apart. since your magneto is fine that just leaves #1 coil....or....#2 cdi box.....to find the coil just follow the wire from your spark plug to it....your CDI box should be mounted under the seat( make sure all the wires are hooked up ) and check again.....
Check output of battery when bike is idling.
If still 11 volt, then your charger, which is the magneto is faulty or the wire is broken from it to your battery. If the charge varies when you test when engine dead to engine idling, wire is fine. Should be 13 to 13.5 volt when idling if magneto is ok.
their is a transistor, the magneto as how u call it carries electricity to the transistor, then the transistor to the ignition coil, and the ignition coil to the spark plug. And yes the magneto is the last to check and rarely see those things gone bad(but things are not made to last jajaja) unless someone opened it and didn't put back the wire correctly that why when u are fixing something u need to mark your wire no matter how intelligent u are, lot of people get the wires confused some connector fit in other places where their are not supposed to be connected, so if at first you market their won't be room for mistake and u will not be misdiagnosing
Ok this is probably one of two things either you have a bad earth on the bike causing a poor re charge rate or your alternator / magneto has gone up the spout ?.
If it is a bad earth you will probably be getting other symptons as well for insatnce rear bulbs blowing or headlight bulbs blowing ..horn or starter ( if fitted ) works intermittently you get the picture . check around the bike to all points where the loom attaches to the frame or the engine ( usually black wire bolted to earth ..= frame ) remove and check wires then clean the area it was attached to with a bit of sand paper / emery cloth and refit especially the one from the battery Minus side Black ?. that will go straight to frame somewhere . If it stays the same after you do this you need to check the output of the magneto . with the bike running place a multimeter on the battery terminals voltages should be any where between 12.volts to 13.5 or higher check specs in manuel if not then Magneto / dynamo / alternator faulty finaly if all else fails ( and this was left till last as you said it was new check the ph of the battery ie sometimes new battries should be full of acid but are not .. just water I have had a few .. especially if they are the none maintanance type . .. hope this helps Regards vortash
Sounds like the stator coil. If your bike has headlights and fancy stuff like that, it has 2 different stator coils behind your magneto or some call it the rotor. sounds like the one that works your lights isnt working right. You can check it with a simple volt merer but you need to know how many omes it should be putting out