Here is my quick guess.... the battery is weak or low and when the fans kick on taking the extra power from the battery, there isn't enough left for the ignition to run properly...

p.s. you should never let a bike idle long enough to get that hot..... these bikes can and will get hot quickly as you are aware I'm sure.

Charge or replace the battery and ride it.... they are not meant to sit idling... If you still having tuning issues, then look at your auto tune and get it adjusted properly.

 

The battery is only 6 months and it holds charge at idle im reading 13.8 and 12.7 with the bike off i check my charging system everything seems good, it is very strange i hooked my voltmeter up to the output wires on the R/R and when both fans are hooked up and they kick on the volts will drop to 12.1 the whole time the fans are on, and it starts missing and running rough like if you were to unplug one of the injectors and plug it back in right away over and over i also am not running a yuasa i was swindled into trying a bike master... ( not gel ) do you think that a lower end battery is not powerful enough by chance?

 

that's strange that the voltage stays up at 12.1 with both fans on... maybe I'm wrong then.

It's also about current too though, and it's clearly an electrical issue from the symptoms though. Do you have access to another normal type battery? If it's holding a good charge and is starting the bike fine, then it should be ok in my opinion.

The only other thing I can think of is a bad ground maybe? Have you double checked the ground wires and also make sure all battery terminal connections are clean and good?

 

yeah that was one of my thoughts as well, unfortunately i dont have access to another battery, ya know these issues started a while back and eventually my generator had went bad the fins on the ends of the stator windings had come off, the shop i took it to said about 5 of them had come off and they knew the history of what was going on and rode it off as that being the issue but even after it was replaced and the R/R was replaced the issue continues ,for the past 2 days i have been disconnecting connectors and adding dielectric grease and i went and checked the the grounds and battery terminals made sure there was good contact i went and checked all the coils, ya know this issue didnt start until i put all my after market stuff on and ended up leaving the bike in the rain for 2 days, but it defiantly is not plugged injectors it has to be electrical, i have been trying to find a good diagram of the ECU plugs so i could start trying to trace back issues from there the ECU is the only thing i have not been able to check and after all i have been through with this issue it has been narrowed down quite a bit to make me believe that it may be the issue... my next question is when your bike starts to experience a higher electrical load than normal (like when the fans kick on) there is a signal sent to the ECU to let the generator/stator know to start working harder? oh BTW thanks for the response bud it is appreciated. :+1

 

Ok, so i have spent some more countless hours searching and reading and mentally exhausting my self to find logic behind the issue and i am going to pull the battery out tomorrow and have it legitimately test and have the CCRs tested i am also going to
recheck the wiring that is closest to the cooling fans, i found that your battery can appear to be functioning appropriately while its on the bike and check out ok with a voltmeter, there is a lot more i want to check but i will start over again from the basics and i could see the battery posing an issue for 2 reasons. the battery was only on my bike maybe a week or two when my stator took a shit and it had completely drain it ( because it was running off the battery alone thanks to the stator) to the point of not even powering an LED and number 2 is its a Bikemaster... maintenance free...lol. After that i am going to double check all the wiring that goes by the radiator fans to make sure nothing has made contact with them by chance. i am also going to open up the Run/Off switch and check the contacts in there and make sure that there is not any over developed corrosion that may have built up.

 

Ok. so i got a new battery today ( yuasa ) and now the bike doesn't misfire at high RPM and its over all performance is better it still has a weird like miss every now and then and it still kind of hesitates/miss/flat spot every once in a while from take off at low RPMs not sure if that could be a dirty injector or maybe it stick a little every now and again but i am in the process of running some PJ1 through it, i was wanting to know if anyone has taken there injectors out and cleaned them and if so is there anything i should be aware of?

 

Glad to know the battery did the trick... I would look at your connections to your ECU and make sure they are fitted well and also maybe put some electrical greese on them to make sure they are getting a good connection.

If you are still getting this and it's consistent... then look at your mapping or injectors... but if it's random... then it's most likely a wiring or connection issue.

 

Ok, so the problem continues.
So what i have done is put it in Diagnostic mode and started looking through them MY TPS D1 is setting at 15 when you first look at it and when you twist the throttle all the way open it is only reading around 50-56 and when you close it it goes back to 19-21 it does not drop all the way back to 15 unless you press the butterfly the rest of the way down, D14 reads 17 at resting and 103 WOT and D15 reads 16 resting and 102 WOT. i have read that D1 is suppose to be 14-21 or so and 101-106 all the way open and when it is not in diagnostic mode put the ignition is on and the kill is set to run the butterfly's will only open roughly a quarter of the way. i was wondering if anyone else bike acts the same way.

 

I had a fluctuating idle on my R1 recently. It was going back and fourth from 1000-1500 rpms. So I did the diagnostic and mine also went to 15 (should be 16) not closing all the way. Opened the throttle and it went to 51 (should be 99). Disconnected Power commander and still 15 but throttle open went to 62. Checked the resistance on the two TPS sensors and the one on the fly by wire read 1.23 (should be 2.0-3.0) the other TPS read 2.6. So I called my buddy at Yamaha who is the service manager and told him what I found. He said that he has never replaced one on a R1 before. Call parts department and they said they have never sold one before. Said they would sell me one for $199. Went on eBay and found one for $35. I figured if they never had a problem before why not go with a used one. Anyway, after installing the TPS I synchronized the throttle bodies. No purpose to sync them prior to troubleshooting the TPS because it won't be accurate.