Starting woes continue - Yamaha FJR Forum : Yamaha FJR Owners Forums
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post #1 of 19 (permalink) Old 08-25-2020, 04:46 AM Thread Starter
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Starting woes continue

Well after the last hunt for the cause of my 06 fjr not starting I thought I'd finally tracked it down to an after market alarm which I bypassed and the bike started up first shot. Haven't had much time to use the bike lately but yesterday I went to start it and nothing, exact same symptoms, dash lights illuminate, solenoid clicks and then there's a phsst type sound from either in the tank or down by the starter but starter does not engage the engine. I tried pulling in the clutch lever and on the second attempt the bike started fine with clutch in. Tired a few more times with clutch in and it started about 3 out of 5 attempts. So I removed the clutch switch, which was covered in gunk inside and out, cleaned it and reinstalled. The bike now starts when the clutch is pulled in and bike in neutral with neutral light illuminated on dash. I also put the bike in gear when running and put the side stand down and the engine cut out as expected so I presume side stand switch is OK.

Any ideas on what to look at much appreciated, bike only starts with clutch in. Really trying the suppress the urge to set the bike on fire...

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2006 GenII
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post #2 of 19 (permalink) Old 08-25-2020, 08:15 AM
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I know this is way too obvious, but it sounds like the battery is weak. And when in doubt, a bad ground somewhere is the root of many electrical problems, but that does not sound like the case here.

Ive never had to deal with voltage regulator problems, but just using common logic that also sounds like it could be an issue. Hopefully the folks here with more experience on older bikes can help.

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post #3 of 19 (permalink) Old 08-25-2020, 08:31 AM
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One simple test of the battery is to charge it, let it sit overnight and see what the resting voltage is in the morning. With voltmeter still connected, check the voltage while cranking the starter.
Starter circuit having to have clutch pulled points to bike thinking it's in gear... neutral light is lit, but...... remove neutral switch (gear position switch), likely oily, clean all the contacts including the spring-loaded brass plunger in the transmission. The switch is behind the shifter linkage, black oval, two screws.
Shifter linkage lube while you're there in case slight misposition is contributing, if sticking may not be in true neutral position.
There's a multi-way connector behind the steering head, ahead of engine that can get corroded, perhaps needs some attention. Was an occasional Gen1 issue.

Ray
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post #4 of 19 (permalink) Old 08-27-2020, 06:43 AM Thread Starter
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Battery is showing 12.7 with ignition off and 12.25 when i try starting, i also bought a new battery and getting same results. While trying to start yesterday it threw a code 12 on the dash, havent seen it do that before, but turning ignition off and on cleared it and bike started after a few prods. I went into diagnostics mode and at position 61 i get 3 codes, 12, 14 and 30. It's starting about 1 out of 4 attempts at the moment so i'm going to get it out of the garage for a run around the block if for nothing else than my sanity as im starting to hate the sight of it in the garage.
Appreciate the help so far.

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post #5 of 19 (permalink) Old 08-27-2020, 08:21 AM
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Sounds like battery is OK. Codes are 12 - Crankshaft position sensor, 14 - Intake air pressure sensor (MAP sensor), 30 - Lean angle sensor. An actual fault 12 or 30 prevent the bike from starting, MAP sensor won't.
Since it does start occasionally, you perhaps have an electrical gremlin. Gen2 has ground spiders, and my guess is those codes are intermittent due to an intermittent connection..... more like a common ground or earth as you call it. I'd recommend checking S4 first as it carries the most grounding load. It is located in the engine compartment.

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While you're in there, you can unplug and re-plug the crankshaft position sensor (on valve cover, right end, connector at throttle bodies). MAP sensor hose can get crud in it, two screws to remove, clean any crud on the vacuum nipple and ensure the hose is clean throughout... it will cause poor running.
FJR's don't like to be started and shut down without warming up sufficiently, fools the ECU into thinking it needs more fuel at startup, thus too much fuel. If that happens, hold the throttle wide open while cranking in say 15 second bursts... A good run up to operating temperature will clear the condition.
As for the codes, I suspect they are false, so clear them and see if they come back. Again, I suspect an intermittent common ground to start with....
If you have ethanol fuel and bike has been sitting, an ounce or two of isopropanol or fuel system conditioner containing isopropanol (Seafoam) will take care of any water that may be sitting at the bottom of the tank... only takes a couple of tablespoons to prevent the bike from starting or running well (can't run on water). If it runs poorly when you go for a ride, this or the MAP sensor hose plugged may be the cause.
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post #6 of 19 (permalink) Old 08-27-2020, 09:01 AM Thread Starter
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Cheers Rayzerman. I've gone through most of the spiders and all looked good, no signs of overheating, and i put a dab of noalox on the spiders. The bike had the s4 recall so i might just recheck that extra wire again. I'll throw some seafoam in the tank and take it for ride and hopefully it restarts again when i fill up at the station.

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post #7 of 19 (permalink) Old 08-27-2020, 09:05 AM
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Seafoam will not correct your starting problems. If the starter is not turning over, it is electrical.

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post #8 of 19 (permalink) Old 08-27-2020, 09:18 AM Thread Starter
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Seafoam is good but its not that good...:-) if only it'd fix my starting issues and than maybe it could cure Covid for good measure, nah was just going to put some in anyway as bike has being laying up for a year which is the funny thing as all these issues have developed while it just sat there. Cheers.
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post #9 of 19 (permalink) Old 08-28-2020, 10:48 PM
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I'm not sure if this will help but I started having intermittent start problems with my 06 FJR1300AS (servo clutch model). I had some battery age troubles over the years and when they start to age and fail to hold a charge one has starting troubles. Eventually I ended up with a buggered starter motor relay. If the battery is weak when the starter relay connects the battery to the starter the current drain from the battery is large and the volts drop which results in the relay solenoid letting go and disconnecting the starter. Volts go back up again and the solenoid tries to operate the relay again and the vicious cycle starts again. Because of the high current draw across the relay contacts during this process there is going to be a bit of internal arcing and sparking between the contacts and this will end up causing pitting on the surfaces making the relay unreliable. No relay switching high current loads will last forever but a poor battery will hasten the process and shorten the relay's life. If you pull off the cover over the battery compartment and try to start the bike and only hear or feel a 'click` with no engine start there is a good chance the starter relay has been promoted to glory. The starter relay is just aft of the battery.
Sourcing a replacement relay was interesting. The price differences were quite startling. I could get one from China for about $12 (delivered free) but this could have taken months to arrive. Most local sources had a price of about $35 delivered and the local Yamaha dealer could supply the genuine part for $140! I opted for the $35 jobbie, fitted it and bingo no more starting problems.
I noted this relay is used on several Yamaha models and it is a generic part supplied to Yamaha from another manufacturer. The part number for the relay is MS5F-631 and it is used by various makers for their motorcycles and small engine vehicles. That number brings up options in costs between $12 and $35.
Good Luck
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post #10 of 19 (permalink) Old 08-29-2020, 07:47 AM Thread Starter
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OK I got to the starter solenoid and shorting it starts the bike each time. Would I be right thinking that points to the start switch or ignition switch as the likely problem with starting?

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