2006 Gen II - runs rough between 2k and 3k RPM...unless cooling fans are running

I know, this is insane. But it's true. I've been going round and round with my bike trying to figure out what this issue is.

2006 gen II

~44k miles

-new plugs

-newish battery

-new air filter

-throttle bodies synched

-fuel injectors removed and professionally cleane

-TPS replaced

-power commander sent into DynoJet - tested good

-valve clearances checked

-same sort of thing happens without power commander - just at lower RPM range.

-no farkles other than brake light modulator.

As you can see, or really mostly hear in the video, between 2k and 3k RPM - (and I think it's mostly that throttle position because I can sort of hear and feel it on the road), the engine stutters, runs 'roughish'. While trying to sort it out with changes to the PC map the other day, I noticed the changes weren't affecting it much. Sometimes they would appear to, but then it wouldn't last. I noticed that whenever the cooling fans kicked on - it was like butter. Sure enough, it's completely repeatable; every time, no matter what else I change. I love to hear any and all theories on this one.

Perhaps you have erratic stator / regulator output in that 2-4K RPM range, and when the fans kick in they suck enough current from the charging system to kinda smooth it out?

if you could find a friend with an oscilloscope and took a 5 second look for strange noise / DC voltage level shifts on the +12v line, that may help explain it.

Just my $0.03...

I'd start checking anything that shares a ground with cooling fan circuit. DC power can do strange things , bleeding into other circuits looking for a ground.

Many problems Gen II with ground issues.

Not a clue?

You mentioned that this happens with or without the Power Commander (although at different RPM). Is this with the PC removed or just all set to zero map conditions?

If not physically and electrically completely removed from the bike, try it before you do anything else.

Otherwise, I agree with mech 1 twa that it is likely some flaky grounding issue. Anything else going on? Try windshield activation, blinkers, hi-lo beam switch, glove box solenoid while fans are running vs not running.

Please make sure that both battery terminals are clean and tight. Good idea to put a voltmeter on the system as well and see if you are running close to 14V fans on or off. Charging system regulator/rectifier, battery condition and connections are always suspect. All the fans should be doing is placing an additional electrical load on the system and possibly drawing down system voltage. What doesn't make sense is that this IMPROVES response. Do the voltage check...

Same issues with Power Commander completely removed.

I am not getting close to 14V, more like 12.8. with the bike running - bad battery or other charging system component? The battery terminals have been gone over with some sandpaper and cleaned with electrical component cleaner and are tight.

I will see what happens if I try the windshield motor and open the throttle at the same time... Who knows?

Thanks for all the feedback so far!

If you are only getting 12.8 with the bike running, you have a problem with battery, connections, regulator/rectifier or (less likely) stator.

What does the voltage do when the fans come on? Given the voltage observation, I think the grounding is less likely but you never know.

Good luck.

Guys, I agree that briefly taking a look at the quality/fastening of ground connectors remains important. Returning to what I was saying earlier, if you could see with an oscilloscope (a volt meter often won't reveal as much), you may have been seeing strange fluctuations in +12v supply as you go off-idle & when those cooling fans come on.

My old Gen 1 puts out 14.1 volts from about 1500 RPM up, so yes, 12.8 volts probably means you have a bad regulator/rectifier.

I would get the running voltage up.

Then I would mod the grounds to the fans, and the headlights while i was there.

Bigger gauge grounds the the main connection at the frame.

I would get the running voltage up.

Then I would mod the grounds to the fans, and the headlights while i was there.

Bigger gauge grounds the the main connection at the frame.

What is the charging voltage when the fans are running? Does it go up (which would explain why it runs better).?

If so, then this isn't an alternator / stator problem. May be the R/R or some weird grounding issue that the running fan helps somehow.

It could also be that the battery is FUBAR and is sucking up all of the charging power at lower rpm.

Can someone tell me where the R/R is on the Gen II bikes?

never mind! I found it.

Regulator/Rectifier tests A-OK, with digital multimeter.

Voltage at idle is actually 13.4 volts and up to 13.8 while running the RPM's up. Initially, multiple tests showed 13.2 volts at idle and then jumping UP to 13.4 volts when the fans would kick on! However, testing again a fifth and sixth time, the voltage remained at 13.4 regardless.

I checked and cleaned every ground spider I could find. They all looked perfectly fine. Still no luck.

In your previous post, you mentioned voltage 12.8 at idle, now 13.4??

Anyway, it is easy to eliminate battery from the equation so I would suggest that next. A known good powersport battery or even a good car battery.

I can't understand what could possibly be happening to have rough running when the fans come on if the system voltage doesn't change!

Thinking out loud - did you try re-connecting the O2 sensor? Assuming that you disconnected it when you plugged in the PC-V, of course. The issue is right in the middle of the closed loop map. Maybe there is some interaction where the ECU is richening up when the fans are on (load compensation) and it is too lean when they are off.

Another option would be to connect an Autotune or Innovate Motorsports LC-1 and see where the mixture is at when it misbehaves.

Well I think you are chasing a bunch of red herrings. First sort out your power system problem. Definitely 13.4 volts at the RR is not right. You should see at least 14.1 volts there and also at the battery if the charging 'system' and battery and DC grounds are good. So as already mentioned, first eliminate the battery as a problem and if that is ok then properly test the RR, both the AC input from the alternator as well as the DC output. Search on the forum here for lots of discussions how to run those tests. If you have eliminated the alternator and RR and battery, then all that's left is your wiring/interconnecting plugs. Once you get the electrical stuff sorted then see how it runs. May have more then one problem going on but I doubt it.

Maybe, but the rough running doesn't really sound like an electrical issue. After watching the video, it sounds more like a fueling issue, particularly since the PCV moves the issue around.

If it happens repeatability as a function of fans on or off, the root cause must be electrical in one fashion or another. Voltage too low or too high, transient signals messing up the computer, flakey grounds etc. Perhaps there are fueling issues but I believe these are the RESULT of an electrical anomaly.

Between the smoothing out with additional electrical draw (fans) and the low charging voltage, it's not a fueling issue per say.

The ECU, etc, needs a minimum amount of amps / volts to run... Low volts will cause all kinds of running issues.

Charge / load test the battery, then hunt down the charging issue-

That is DEFINITELY an issue which needs addressing first..

Basic's first...