2006 died on freeway on way home from trip

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Have you checked the 15A fuse (I) in the wiring diagram? Check the brown/blue wire for power with the key on. That wire feeds 6 of those fuses from the ignition switch.

I would second the notion for checking the ignition switch and ground spider recalls.
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When the bike died, was it instant or a loss of power and then dead? Electrical stuff like a bad kickstand safety switch will usually instantly kill the bike (I know from experience), but a fuel pump failing will be a relatively slower death. I can tell you from my 07 that there's a fuel pump relay under the headlights that you can reach from above the front fender. Mine had corrosion on the connector contacts.

I'm not clear on whether you hear the fuel pump run like it always does when you turn the key on? If not, grab the electrical schematic and start checking for power at easily accessible locations until you narrow down where the break in the circuit is located. I know, easier said than done with difficult to access components. :(

 
Ignition switch replacement was done by the gentleman who owned the bike prior to my owning it. He had all the documentation in addition to being a super-above-board guy, and they didn't match the fuel tank...so I have to deal with 2 keys.

Do you believe it to be the key even when everything else that it is supposed to do works fine? Turns on, cranks, powers lots of stuff...just won't start because it is apparently not supplying juice to the fuel system.

Is there a way to test the ignition switch?

 
Bike was running like you would expect an FJR to run; perfectly and without a hiccup to indicate that anything was wrong. Spent the night in Taos and took off in the morning traveling through Las Vegas, NM and on to I-40 east. Got on the freeway and about 10 miles west of Santa Rosa, NM the bike lost power for a moment and then caught again like nothing was wrong. Gauges stayed on and everything seemed good; it felt like I had just run out of fuel when it lost power. Traveled a few more miles with no problem and it did the same thing a couple of times before dying altogether.

The thing that confuses me the most is the suddenness of the episode. Considered that it might be bad fuel, but it is the same fuel that I had been using for the previous many miles without incident, so I dismissed that idea.

 
There is a "relay unit" up in the nose where a number of starting interlocks join up. This has been an issue with a few bikes. Once you have verified that things like the sidestand switch and gear position switch etc. are OK, it may be worth checking the relay unit (or coupler).

The "snip" (below) from the FSM may be a help.

Not 100% sure but I think it is #21 on this fiche

https://www.partzilla.com/catalog/yamaha/motorcycle/2006/fjr13abs-fjr13av/electrical-2

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Thanks Ross,

That's where I'm headed next I think. Was hoping that I could find the culprit without pulling the plastic, but oh well. There are a couple of things I could do while I'm there anyway.

The situation where the ECU is not registering battery voltage seems to be an indicator that it could be the problem.

Reading in the diagnostics suggestions in the manual, replacing the ECU is the 'when all else fails' solution. If that is the solution I end up with, can I put a flashed ECU in and lose my power commander?

 
Power Commander??

Try bypassing it before you do anything else!!

I may have missed it but does the engine turn over but no start? Or not even turn over?

 
If there's a PC installed try disconnecting it and putting the back straight through. I have heard of PC failures causing problems. On the hand control and side stand kill switches I don't remember if the FJR will turn and not start or not turn at all (different bikes do either).

 
FJR will not turn over if sidestand switch is open, or if bike is in gear without clutch pulled.

- so unlikely to be the diode relay unit.

 
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It is grounded to a fuse block that is grounded to the negative terminal on the battery.

I did change that connection when I added the fuse block, but I did a really good job of it. Tinned the wire before landing it at the block. The fuse block is an Eastern Beaver PC-8 under the seat and fired through a relay. Everything else on the panel is working perfectly.

The Power Commander was on the bike when I bought it. If it needs to be grounded straight to the battery, I didn't know that and it's been this way for quite a while.

It might sound like I'm being argumentative. If I am coming across like that, nothing could be farther from the truth. I am reading your great advice and trying to answer with things that might be pertinent. I really appreciate your taking time to help me.

 
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slatonp4, It's all good, it's just that the instructions for the PC install specifically calls out to connect the ground to the battery terminal. There are some accounts that site strange action of the PC when not grounded to the battery terminal. But there are others that have done it differently that had no problems. I just thought it might be something quick to swap/check. It sounds like it might be easier to just bypass the PC. At least you'll isolate that as good or bad.

Does the starter crank strong when you try to start it? I know you said the battery is new, sometimes they can fool you.

Before you tear everything apart to get to that Fuel Injection Relay, check for power going to it from the fuse box.

Sorry I don't mean to second guess your efforts, just trying to throw out stuff I might try in your shoes. Think Positive.
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Trust me, I don't feel second-guessed.

Starter cranks nice and strong. Ran the battery down a little trying to get it started, but put it on the charger and topped it back up.

Not really too frustrated so far. I was hoping it was something simple, but this is serving to justify the expense of making the last few miles home. Funny how, with the UHaul, the tow, and all the extra fuel, the last 750 miles wound up costing more than the rest of the entire trip combined. The nice thing about it is that ALL of the good riding was pretty much done once I hit I-40. Rest of the trip was phenomenal and the bike just made me love it more. These FJRs rock!

Again, thank you.

Paul

 
Thanks Ross,
That's where I'm headed next I think. Was hoping that I could find the culprit without pulling the plastic, but oh well. There are a couple of things I could do while I'm there anyway.

The situation where the ECU is not registering battery voltage seems to be an indicator that it could be the problem.

Reading in the diagnostics suggestions in the manual, replacing the ECU is the 'when all else fails' solution. If that is the solution I end up with, can I put a flashed ECU in and lose my power commander?
That relay unit (that had corrosion on the connection on my 07) is accessible without removing anything. Visualize your head just above the front fender, between the fork tubes and looking forward. This relay is just above the lower edge of the nose cowling. You can actually see it without removing your head and sticking it in the position I described.
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You can reach in there and slip it out of the rubber holder (similar to how other relays are attached to the bike) and pull it backwards and disconnect the connector to inspect for corrosion and also check power and/or continuity.

added on edit:

Looking at the FSM, this relay is a combination of part of the interlock with the start/stop switching AND the fuel pump relay. For the fuel pump to run consistently you should have voltage at the red wire and a good ground on the Red/Blue wire (through the fuel pump) and no corrosion on any contacts. Due to the potential for corrosion on some pins, part of this relay module may work but other functions don't work.

 
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Couple of pics that might help.

I drew out the circuit around the relay to try to better understand what it's doing. This is for YCCS version, but I think you can simply ignore the bits associated with that.

(Click on image for larger view)



Its position can be seen in this picture, it's that rubber protected thing with a big bunch of wires going to it.



 
I don't thenk the Gen2's have any rubber boot. On a recent ride with Powerman, he said he was seeing the neutral light flicker. This is another symptom of that relay going bad. He had a spare with him, but when we stopped and pulled it there was corrosion in the connection. He cleaned the connector and installed the new relay and symptom gone. When I had the same issue on my '07, the relay would chatter. I could hear it when I turned the ignition on. I also experienced the neutral light, but also experienced engine stumble. There was no corrosion on mine. The relay was just failing. Your problem could be as simple as that. If that relay completely craps out you lose the fuel pump.

 
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