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Whichever valves are loose when the mark appears in the window - adjust them. Due to the pressure by the opposite cylinder's valve springs, it will want to rotate past the TDC mark. Then, rotate one half turn and the other cylinder's valves will be loose. Then adjust them and spin the crank a ferw times and re-check the clearance. Don't want one valve ticking louder than the others once you start it back up. You need not go strictly by the cam marks, but by crank position.
 
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i prefer the "lobe up" method, setting each individually, rotating crank where necessary to achieve positions.
 
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i prefer the "lobe up" method, setting each individually, rotating crank where necessary to achieve positions.
Yeah, the cam sprocket marks are kinda like the swingarm marks.
 
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Just be sure the cam lobes point away from the rocker arm . The cams are round but for the lobe. You can adjust the valves any where the tha lobe is pointed away from the rocker arm

Fog
 

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Discussion Starter · #25 ·
Thanks for all of the help gents. I have successfully completed the task and set all valves to spec. You guys were right they were grossly out of spec. I was able to get her back together and it fired up smoothly and was able to get rev passes for 4K rpms without it dying. Here is where I am now:
after assembly I connected an auxiliary tank to get ready for carb syncing. I wanted to fire it up to see if there was any impact from adjusting the valves clearances and it was running smooth. I was able to go beyond 4K rpms without any issues. As I was dialing in tue idle speed I noticed I forgot to cover the vacuum hose on the left carb. As soon as I covered it up it started to run horribly and I couldn’t get it to idle correctly. So I left it uncovered for a bit and it was right back to running smoothly. I covered it again and It ended up dying and now it won’t start. I left vacuum line open again to replicate the setup that was working but now it won’t start. I did notice my battery has drained after a few futile attempts at starting so I’m going to charge the battery and see if I can’t get it going again.
Assuming the reason it won’t start now is the battery, what do you guys think could be causing such drastic differences in running conditions with the vacuum hose being open vs closed? I know when I do the carb syncing I’ll have those lines going into the synchronization mechanism so my thoughts would be that it would run horribly since it did not respond well to having the line closed.
 

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Discussion Starter · #30 ·
Here are some updates: I’m able to get it started but looks like my right side carb on cylinder 2 is running a bit rich? I’m seeing dark smoke and it smells like fuel coming out of the right side exhaust but only the right side. I did remember the spark plug on that side having a bit of unburned fuel when I was doing the valves. I have it set to specs found in other posts but perhaps I need to adjust the float on that side a a bit more?
 

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How do the plug and wire (at both ends) look? Did perhaps the needle jet of the (R) carb fall out or not get replaced?
 

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Discussion Starter · #32 ·
The plug is brand new it was replaced wire looked good as well but I’ll double check them and test the coil. When I took off the coil on the right side to do the valves I noticed the leads from the harness to the coil had some build up on the connectors so I cleaned them a bit but maybe im thinking might be good to double check those are making a solid connection.
I double checked and the needle is there but I didn’t replace it during the carb rebuild. Should I replace it? Or is there a way to make sure it’s in spec?
 

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You can go to the coil-on-plug conversion. - cheap and easy - or just trim about 1/4" off each end of the plug wires and re-connect. A little silicone spray will keep water out. As to the connectors, get some pipe cleaners. They are cheap and abrasive enough to clean the insides of the connectors, along with a little electrical contact cleaner, or even alcohol, then blasted out with compressed air or even computer duster.

If the right side runs rough and only clears up when you're gassing it, the right side needle jet might have fallen out - if you tore the carbs down.
 

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Discussion Starter · #34 ·
You can go to the coil-on-plug conversion. - cheap and easy - or just trim about 1/4" off each end of the plug wires and re-connect. A little silicone spray will keep water out. As to the connectors, get some pipe cleaners. They are cheap and abrasive enough to clean the insides of the connectors, along with a little electrical contact cleaner, or even alcohol, then blasted out with compressed air or even computer duster.

If the right side runs rough and only clears up when you're gassing it, the right side needle jet might have fallen out - if you tore the carbs down.
I’ll do that today and see if there is any change but gassing it doesn’t clear the issue. Gassing it kills the bike. As soon as I open the throttle it starts to sputter and then dies and you can smell fuel as well as see dark smoke coming out of the right exhaust. This makes me believe that the right cylinder is not firing properly and as a result fuel is not combusting which is allowing fuel to enter the exhaust. I’m hoping cleaning the contacts does the trick but given that this bike was untouched in a garage for 7 years I feel like there might be something else I’m missing.
 

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I’ll do that today and see if there is any change but gassing it doesn’t clear the issue. Gassing it kills the bike. As soon as I open the throttle it starts to sputter and then dies and you can smell fuel as well as see dark smoke coming out of the right exhaust. This makes me believe that the right cylinder is not firing properly and as a result fuel is not combusting which is allowing fuel to enter the exhaust. I’m hoping cleaning the contacts does the trick but given that this bike was untouched in a garage for 7 years I feel like there might be something else I’m missing.
You can tell if the right cylinder is not firing from the temperature of the header. Use one of those laser temp guns, or spritz a mist of water onto the header to determine if it's getting hot.

If the engine is only running on a single cylinder it should sound quite horrible and lumpy.
 

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Discussion Starter · #36 ·
You can tell if the right cylinder is not firing from the temperature of the header. Use one of those laser temp guns, or spritz a mist of water onto the header to determine if it's getting hot.

If the engine is only running on a single cylinder it should sound quite horrible and lumpy.
The right side is definitely firing. The headers are both hot. I confirmed after reading your reply. I’d like to see if there is a variable in temperature from the left cylinder to the right. Perhaps the right side is not firing as well as the left?
 

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Try disconnecting the right hand side (#2 cylinder) vacuum line at the carb. Apply vacuum to see if the Pair Valve is holding vacuum.
 

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Discussion Starter · #38 ·
Updates: tested coils and spark plug caps and found them all to be within spec. I had an extra set so swapped them for new ones just in case and then checked the headers and found that both were warm but the right side is much much hotter than the left. I think it’s time for a compression and leak down test which I probably should have done before I started work on the bike 🤦‍♂️ let me know if you guys think there is something else I should dig into.
 

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Discussion Starter · #39 ·
im closer to finding the issue, I checked the compression wet and dry and they were in spec but there is no spark on the left coil when I ground the spark plug to the engine. I do see a spark jump from the central electrode to the engine casing if I don’t Ground the plug to the engine so it looks there is power but not sure what to look for here. My guess would be to check the cdi and the input output voltage to the coils as well. But if I’m seeing a spark when it’s not grounded doesn’t that mean there is power? Could this be caused by some bad grounding maybe? Or is this a sign of a poor continuity in current to the left coil. The battery is fully charged by the way.
when I test the right side spark I get a nice healthy spark between the central electrode and the ground electrode when I ground it to the side of the engine as expected.
 

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Discussion Starter · #40 ·
Ive tested the harness and I am getting equal voltage readings on the coil leads going into the cdi. So it appears the issue lies within the cdi and should be replaced. Quick recap for anyone still keeping tabs

2006 500r 5,142 miles
Garaged for 7 years

PO had no history on the bike since it was passed down to him. Bike was full of rust an in pretty bad shape but complete.

first I cleaned the tank and got rid of the old fuel and rust inside the tank.

Rebuilt fuel petcock as it was leaking
Rebuilt gas cap and modified vent
I did a carb rebuild and cleaned them thoroughly. After reassembly fired her up and all was good both cylinders firing, both were warm to the touch and was enough for me to “confirm” both cylinders were firing. After letting the bike warm a bit I pulled the throttle and the bike would die every time it got to 4K rpms. I checked the valve clearances and they were out of spec so they were adjusted and was fired up again after reassembly and it ran great for minute I could beyond 4K rpms after a few minutes there was a sudden “hiccup” and the bike started running horribly again. It wouldn’t start and I could see dark smoke that smelled a lot like fuel out of the right exhaust. This led me to believe I had a carb float issue and was running too rich but decided to do what I should have done before and test the compression and health of the engine followed by testing ignition system, coils, caps, plugs, and cleaned all of the leads as they were full of build up. Everything checked out that left two possibilities, bad lead somewhere in the harness to left coil or bad cdi. After testing the leads to make sure I was getting equal voltage into the cdi. I’m left with my conclusion of a bad CDI. Biggest takeaway- don’t skip ahead and methodically test your components and systems one by one to ensure everything is functioning as it should. This is my first foray into a restoration and first time ever putting a wrench to a bike and it was a lot fun learning about all the mistakes I made. Thanks for everyone’s help and I hope this helps someone.
 
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