Ok so I have had the error 46 code twice now (5 years apart) and have used this forum and other sites to determine what the problem was , so thought i would collate everything into one post so others could fault find the issue easier.

So first things first is I would urge everyone to install a battery charge monitor light to make you aware of an issue BEFORE you get stranded at the side of the road with a dead battery.
something like this .

https://www.ebay.co.uk/itm/LED-MOTOR...-/200609174686


If you get the engine warning light and it results in error code 46 then it is a battery issue.
to fault find.
first things first. you require a Multimeter.
then test the battery , charge should be above 12v
and then test the charging system.

here�s how.

https://www.youtube.com/watch?v=1j9TXdIhInM

If the battery isn�t charging the first thing to check id the Reg/Rec plug. if its corroded or damaged then it may be issue. here�s how to change it.

https://www.youtube.com/watch?v=eHlpMSPzJQs

The connecter can be sourced by googling the part number RM14105R.

you can get them on eBay but cheaper here.

https://kojaycat.co.uk/epages/950000...oducts/KYG6WAY

Next step is to test the reg/rec itself to determine if its Gubbed or not.

Heres how.
https://youtu.be/-2jWIkhy1fo

and also how to test the stator whilst you�re at it.

https://youtu.be/NSV8iU65bH8

and here�s a link to the workshop manual. page 8-56 for stator values.

http://www.xt660-club.hu/Media/Yamah...ere_Manual.pdf

Also last word on this issue is resealing the badly designed plug.
I haven�t been able to determine for certain that silicone is non conductive to reseal the plug to avoid water ingress. A friend who builds modular synths tells me that Hot glue from a glue gun is non conductive, if you don�t have one then i would also recommend .

https://www.screwfix.com/p/self-amal...SABEgLRGPD_BwE

Top Man!!!..Its posts like this that forums are all about.

Man,I can hardly believe this...
It just happened to me today...
Red light and error 46 on the dash...
And it was two days after a rainy ride (not to long,7.5 km...)
I will start measuring everything (as long as I find some time...)

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OK,found some time so here it goes:

Habits have changed for the owner,and as he is a seven and a half years old daddy,riding Ektor (my xtx that is) is not the first priority...
I have reached the scenario of around 40 km per week...

The battery is a GS GT9B4,exactly two and a half years old.
The usage therefore charging of it is little.
I made a 7 km ride in rainy condition,two days before error code 46 appeared on the dash (don't know if it is related to it but I have a suspicion)
I managed to get access to a Ctek mxs 5 to charge the battery.
It brought it back to life. (12.9v on open circuit)
In the meantime I measured the reg/rec as per the video from the tube.
It was healthy.
I asked Spiros Samios (the guy that remaps our ECUs) and he blaimed the very little usage of the motor.
Put the bat back to it's place,checked all fuses and connections for shorts and rust (nothing at all)
Cranked it and everything was OK,like nothing ever happened...
Charging on operation was 14.2v (idle) to 14.6v (revving high)
Charging system works perfect.
Do you think it is the low usage of the motor that occured it?

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