2001 r6 with 20000 miles. I have rode this bike all over and never had any problems. I do the maitenance regularly. Carbs, oil, replace clutch and so on. I was riding today and all of the sudden at idle it shut off. I thought nothing of it started it back up and went on my way. Finally when i pulled into a parking lot it shut off again and when i tried to start it it just clicked and sounded like the battery was dead. All gauges and lights did work. Finally after a few minutes everything was dead. I tried rolling the bike and poping the clutch. It ran for a minute and i was driving it then the gauges went blank and a few seconds later it started backfiring bad at about 40mph and it shut off again. I have the bike apart now and am trying to test stator, regulator, rectfier and so on. I dont think it would be the battery, it seems worse than that. Its got to be electrical right. Please give suggestions what it could be and the proper steps to check for problems. While its apart i guess i go ahead do fuel filter, oil, plugs, air filter, and clean carbs again. I also tried jumping it from another vehicle today and i got nothing but a fast clicking noise.

You probably have a bad plate in your battery causing a dead short. You can check the stator and rectifier to rule them out, but I would bet heavily that it is your battery.

I'm thinking rectifier but as per the previous post eliminate the battery first. The symptoms you are describing would indicate you were driving on the battery until it got to low to run the bike: lights on and off on the dash, backfriing etc.

By the way, the bike should have started no problem with a boost if the problem is the battery, the rectifier or the stator. None of these will stop it from starting. I'm thinking bad connection on one of the booster cables.

Charge your battery and make sure it is reading above 12 volts. Start the bike - I'm thinking it will start right away. If it does, check the voltage at the battery. At an idle it should be around 12.5 or slightly higher. At 5,000 rpm you should read 13.5 volts or higher. If not I would check all the connections at the rectifier...these are problematic with early generation R6s. If this is ok, then check the connector between the alternator/stator. Usually three white wires from the alternator to the connector - I have seen these burned as well.
If all this is ok, then swap out the rectifier and or test the alternator windings as per the shop manual.

Post what you find and we can help from there.

Hey. I know this post is kind of old but I have been having the exact same problems. I have a 2000 r6 and I have since replaced the rectifier, the stator and the battery and I am still having the same problems. Please someone help me out!!

You are in the same boat I'm surrently in. Sadly the only thing left to check for are shorts and broken wires along the system. I started at the headlights and found both of my headlight plugs were shorted and burned up pretty crispy.

When my problem first started I would run and charge at about 11v. This is a problem, I tested the battery and found it wouldn't maintain a charge. It would charge up to 12.8v no problem but if you left it unhooked and tested it the next day it would be down to 11.5v, so I replaced the battery. Next I tested the stator, per the Yamaha Factory Service Manual the pin test failed getting resistance of .4ohms across the one set and .6ohms across the other pair instead of the desired .33ohm threshold. I replaced the stator with a unit from RMstator.com that is supposed to produce 120% of OE voltage, I thought this would be a perfect upgrade and allow me to use a heated vest in the winter. But after the new stator I still get .4ohms and .6ohms across the sets of pins?!?! wtf, right? Oh well, now I'm charging at 12.2v which is still lower then spec. I did a pin test of the rectifier and that checked out okay, I think I'm still going to replace it due to the age, my skepticism, and the bike has over 50k miles. Hopefully that will solve it.

If I were you, I would also check all you plugs to make sure they are shorting out and check your other components. You might have a starter that is pulling a draw due to a fault and the charging system can't overcome it.

mine was doin that same thing and my wires going to the rec/reg were all corroded and brittle. i just cut it where it wasnt corroded anymore and ran new wires to the connector to the rec/reg. ran great after that untill my piston and valves got in a fight