2006 Yamaha R6 turns off when shifted into gear

[Shaggy]

2006 Yamaha R6 race bike with a 2007 engine. Bike is a cripple 450.

I recently did a keyless ignition swap and when I wired the toggle switch, I accidentally ran the wires incorrectly the first time I put it all together. This blew the neutral switch in the back of the tranny. I confirmed it was the issue by grounding the wire, which activated the neutral light. I replaced the neutral switch with a Yamaha OEM part and now the bike will correctly show neutral and start in neutral.

However, when placed into gear the bike immediately turns off. It also won't start while in gear with the clutch in.

I'm assuming there is some kind of theft prevention measure, much like the neutral switch, that I'm missing. Perhaps something related to the clutch?

Any help is appreciated.

 

[cheez]

Sidestand switch?

Edit: I guess "race bike" implies sidestand switch/clutch switch/other nannies have all been overridden or are not present?

 

[Shaggy]

Went into Diagnostic Mode and pulled the following codes, but have no idea how to read them:

d01: 18
d02: 98
d03: 99
d05: 88
d06: 145
d07: 0
d08: 0.6
d09: 0.0
d13: 17
d14: 16
d15: 15
d20: on
d21: on
d30: 00
d31: 00
d32: 00
d33: 00
d36: 00
d37: 00
d38: 00
d39: 00
d40: 00
d41: 00
d42: 00
d43: 00
d48: 00
d50: 00
d51: 00
d52: 00
d53: 0
d60: 00
d61: 13
d62: 9
d63: 00
d70: 0

 

[Shaggy]

Sidestand switch?

Good idea, but there is no side stand since it's a race bike. I'll dig around and see if I can find how the switch was removed.

 

[I Use Dial]

Tilt sensor?

 

[Shaggy]

So.... in Diagnostic Mode, if I put the bike in gear, both the Neutral Switch and Sidestand Switch change from “On” to “Off”, even though there is no Sidestand Switch. That seems curious to me, but no idea what it means.

 

[Shaggy]

Tilt sensor is reading and functioning correctly, and that would not explain why it will start and run in Neutral, but not in gear (right?). I unbolted it, verified that it was functioning by watching the readout change in Diagnostic Mode, and then reinstalled it. Bike still won't run or start in gear. I'm thinking it has something to do with the clutch safety switch or side stand switch. Still working on those....

I pulled the following codes after doing more research on how to use Diagnostic Mode:

13 - Intake Air Pressure Sensor: Open or Short
14 - Intake Air Pressure Sensor: Hose System Malfunction
15 - Throttle Position Sensor: Open or Short or Loose Connection
17 - EXUP Servo Motor Circuit: Open or Short or Loose Connection
21 - Coolant Temperature Sensor: Open or Short
22 - Air Temperature Sensor: Open or Short
23 - Atmospheric Pressure Sensor: Open or Short
41 - Lean Angle Sensor: Open or Short
59 - Throttle Position Sensor Cable Pulley: Open or Short or Loose Connection

I cleared the codes and there is no change in behavior from the bike.

 

[295566]

I'm assuming it's similar to my old R1, which had 3 conditions for starting.

• If the kickstand was down, bike had to be in neutral. Putting kickstand down in gear would kill the engine, regardless of clutch in or not.
• The bike had to be in either neutral, or have the clutch pulled in, to start.

To clarify, were the kickstand, neutral, and clutch all bypassed before the keyless swap was done? Or was this all done at the same time?

I'm thinking the sidestand was bypassed incorrectly, and is reading as permanently down, killing the engine when you put it in gear.

 

[I Use Dial]

I've never messed around with a tilt sensor, so I don't know its full function (does it kill the bike, no matter what, or only if in gear?), but when you say "race bike" I think "crash" and I think "tilt sensor" because it's easy to forget about.

 

[dowlinginchico]

People can do crazy things to bikes, do you think the side stand wires were wired to the neutral switch? To avoid throwing codes?

I'd look closer at the side stand wires. If the side stand switch is gone, how can it switch from on to off? Is it wired into another switch?

 

[Shaggy]

The strange thing is that this was not an issue before I messed up the wiring in the ignition toggle. I even plugged the old keyed ignition into the harness and the issue remains, so I know its not the switch. Something must have happened when I crossed the wires incorrectly....

I’m still digging around to find the side stand wiring.

The clutch switch is also gone, so no clue how that was bypassed yet.

 

[Shaggy]

I've dug around under the tank for the last hour and can't even find a connector for the side stand switch. I'm stumped....

 

[295566]

Looks like it should be a connector coming off the relay units, with a blue/black wire coming out, and a black wire going to ground. The sidestand switch should plug into that. It's a blue plastic connector (both ends)

Service manual download here.

 

[Shaggy]

No plugs matching that description. This bike has been a race bike since Day 1 off the lot and it’s been through 3-4 hands, sho who knows what’s been done. :dunno

I think I found the issue. I was doing resistance testing on the relay box and there were some diodes with no continuity. I’m hoping that’s the issue. I ordered the part, but it won’t arrive for about a week.

 

[cheez]

No plugs matching that description. This bike has been a race bike since Day 1 off the lot and it’s been through 3-4 hands, sho who knows what’s been done. :dunno

I think I found the issue. I was doing resistance testing on the relay box and there were some diodes with no continuity. I’m hoping that’s the issue. I ordered the part, but it won’t arrive for about a week.

Good luck- hope you've got your gremlin identified.

 

[Shaggy]

The set of wires without continuity were Blue/Black and Blue/Yellow, which could runs to the Clutch Switch if I’m reading the wiring diagram correctly.

If that circuit is broken, that might explain the issue.

 

[stangmx13]

u dont need to bypass the clutch switch on an R6 race bike. the left bar switches can just be removed, which take the clutch switch with them.

sounds like your side stand circuit is busted. its wired right next to the neutral switch and does include a few diodes.

 

[Shaggy]

The bike does not have a clutch switch on the handlebar, but the circuit in the relay appears to be busted for some reason.

I’m not getting any continuity reading between prongs 5 and 3 according to the service manual instructions, but all others are getting ~700 Ohms.

 

[Shaggy]

To clarify, were the kickstand, neutral, and clutch all bypassed before the keyless swap was done? Or was this all done at the same time?

Sorry... I missed this question. All I did was eliminate the key ignition (albeit incorrectly at first). The neutral switch was somehow blown by my wiring mistake and I’m assuming it is a default response for theft attempts.

The side stand switch was bypassed previously and I didn’t mess with it. The clutch lever switch was removed at the connector previously and I didn’t mess with it.

The relay assembly and tilt sensor are on the way. I’ll update progress when they arrive.

 

[Shaggy]

Tracked down the wires for the side stand switch. They were snipped super short and tucked under the main harness waaaay back by the ECU. The connection seemed fine, but I re-spliced and soldered them to be double sure. Still won't start in gear.



I'm pretty certain it's the relay box. Looking at the wiring diagram, here is what I'm hypothesizing....

The crossed wires at the Main Switch (3) sent the wrong voltage through the Blue/Yellow wire into the Relay Box (15). The directional arrows going into the Relay Box show that the next point of contact is the Neutral Switch [Blue wire (E) into (16)] and Blue/Black wire into the Side Stand Switch (17). I think that's why the Neutral Switch got blown (and probably the relay for the Side Stand Switch also).

The resistance checks confirmed that the only failure in the Relay Box was between Blue/Yellow going to/from the Main Switch and Blue/Black going to/from the Side Stand Switch.

So, I'm hoping that a new Relay Box will fix the problem. Ugh....... I hate electrical stuff.