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Discussion Starter #1 (Edited)
Got a check engine light while riding and luckily made it home. I read up on code 46 in the manual (2003 R6s) and started testing. The battery(AGM) was dead, so I charged it back up to 12.8v then started testing. The first time I turned on the bike the voltage dropped to 11.8v and stayed there regardless of throttle input. I turned it off and followed the manual for testing the stator. The stator wires look good, none had continuity to ground, and the resistance between all of them was .3ohm. According to the manual, that rules out the stator. I unplugged the regulator/rectifier and tested it for forward and reverse bias. I tested both power and ground connections to all the 3 leads and they showed either OL or .5v. The only weird thing was that the rectifier body didnt have continuity with any other grounds on the bike (frame or neg on the battery).

I turned the bike on again just to check, as all 3 parts of the charging system seem to be operational. It started with 12.6v and dropped to 11.6v. however, after a few moments and a bit of reving the engine, it jumped up to 16.8v at idle and 17v at 5k rpm. Any other tests I can do to narrow down the issue or is there anything I did incorrectly? Could this be a grounding issue or is the regulator just failing in a weird way or are both the regulator and stator on the way out?

Just a side note, for the last couple years I haven't been riding much and its been hooked up to the deltran tender or the CTEK tender for months at a time.

If its the regulator or stator, any reason not to pick up a working used one for less than a 1/5 of a new one?
 

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well the regulators job is exactly what it sounds like. regulating the voltage to the battery during operation of the engine. it if is going above the 14.5 v it's not doing it's job. over charging a battery is as bad as not charging it. it will kill it. probably even faster than not charging it.
I would replace the regulator for sure. personally, I would never buy used electronics. the only reason i would buy a used piece of electronics is if yamaha quit making it and no aftermarket parts are available.
ricks motorsport might make one for it. usually less $ than yamaha.
 

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Any changes from stock? Insufficient/damaged grounding can prevent a charging system from regulating its output, resulting with damage to itself. "Voltage drop testing" can be used to spot bad connections. With all circuits loaded to/near their potential, measure drop between clamp and battery negative post; body and battery negative post; engine and body negative post.

Do not charge your battery while it's connected to your vehicle.
 

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It started with 12.6v and dropped to 11.6v. however, after a few moments and a bit of reving the engine, it jumped up to 16.8v at idle and 17v at 5k rpm.

Sounds very similar to what happened on mine. My rectifier was reading 0.5v, 0.48V, 0.5V, so not all the same, but close. Your regulator seems bad. At no point should the DC output exceed 15V.
 

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Got a check engine light while riding and luckily made it home. I read up on code 46 in the manual (2003 R6s) and started testing. The battery(AGM) was dead, so I charged it back up to 12.8v then started testing. The first time I turned on the bike the voltage dropped to 11.8v and stayed there regardless of throttle input. I turned it off and followed the manual for testing the stator. The stator wires look good, none had continuity to ground, and the resistance between all of them was .3ohm. According to the manual, that rules out the stator. I unplugged the regulator/rectifier and tested it for forward and reverse bias. I tested both power and ground connections to all the 3 leads and they showed either OL or .5v. The only weird thing was that the rectifier body didnt have continuity with any other grounds on the bike (frame or neg on the battery).

I turned the bike on again just to check, as all 3 parts of the charging system seem to be operational. It started with 12.6v and dropped to 11.6v. however, after a few moments and a bit of reving the engine, it jumped up to 16.8v at idle and 17v at 5k rpm. Any other tests I can do to narrow down the issue or is there anything I did incorrectly? Could this be a grounding issue or is the regulator just failing in a weird way or are both the regulator and stator on the way out?

Just a side note, for the last couple years I haven't been riding much and its been hooked up to the deltran tender or the CTEK tender for months at a time.

If its the regulator or stator, any reason not to pick up a working used one for less than a 1/5 of a new one?
I can help you , had a issue like this on my bike for weeks now
:
Wanna be sure its your rectifier , do this diode test >>
you will need a multi-meter .. follow the steps in the video , and it will determine if its a recitifier issues

OR
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PLUG off your stator coupler at the side of the bike ,do a continuity test on the 3 pins ..meaning postive into white lead 1 to white lead 2 , white lead 2& 3 , white leads 1 & 3 --so three test in total - post the results below on the
OR_
PLUG your multi meter leads from the back of the recitifer while bike is on and running , you should see 3 wires and a red wire and black wire (5 in total)
plug multimeter positive to red
plug meter negative to black

post results on idle and at 5k , and over 5k below
 

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Discussion Starter #6
Thanks guys. replaced the rectifier with a used oem one. the voltage is now 13.6 at idle and at 5k rpm. did a few test drives and the battery is 12.8v before and after test drives. everything seems ok and tests ok despite the voltage not quite hitting 14v at 5k rpm. Will leave it for now and see how it goes.
 
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