81 XJ650 Misfiring After Heavy Rain - Coils Replaced

I got caught in a severe downpour two days ago, and the bike began to misfire at idle. Was able to limp home by keeping my revs up, and I expected that the problem was just wet ignition coils. The misfiring seemed to die out and go away when at high RPM, strangely enough.

However, I decided to test that hypothesis by finally installing the dyna coil kit I bought from chacal a while back. The install went well, but alas, the bike is behaving exactly the same as before the coil replacement. I tried draining the gas out of the tank and carb bowls, then firing it up on an auxiliary tank, and the same thing happened.

Pulled the plugs, and all four appear somewhat sooty. If it is the ignition, it doesn’t seem to be restricted to just one coil. Where could water have gotten that would cause this?

Edit: got a video of how it runs - https://youtube.com/shorts/30D4kGpUWyc?si=tHw1feaz8qB2p6-Q

 

Wiring nearest the road, if all four cylinders the black earth wire from the pick up coils to the TCI in plug. Check all connectors spray with a water repellant follow the wiring testing the voltage at the pigtails going into the coils. Check charging system and electrical connectors from the alternator brushes black and green wires. If you can get it started rev the engine and set a multimeter to 20 volts DC and check if you are getting around 13.5 volts from the alternator. Wiggle the wiring too while pressing the starter might be a loose connection.

 

The alternator does not kick in until revs reach a minimum of 2000 rpm. Do you have the original Yamaha fuse box? If so change it for a blade type. Make sure there is no dampness below the spark plug caps. Apply a little dielectric grease on the rubber to cap joint and the lead to cap joints. My CB750 misfired in the wet so l used the dielectric grease to protect the joints from water ingress.

 

When I replaced the coils, I replaced the plug wires and caps too, so I know there isn’t water trapped in there. Though, I could still benefit from more dielectric grease on the outside of the joints. I used grease when putting the caps on after trimming the wires to fit, but only a slight coating on the wire to help the plug slide on.

I will definitely still check the alternator and that ground pathway. I bought a can of DeoxIt D5 for my vintage computer hobby, and the stuff comes in clutch for electrical connectors.

I’ll say though, I do have some additional data. I used a colortune plug in all four cylinders to see the misfires, and it looked like I was still getting spark when the thing wouldn’t fire. I was able to get it to smooth out somewhat (not perfect) by adjusting the idle mixture screws. Is it possible that water seeped into those screws and inhibited fuel flow?

 

Mixture screws have a small o ring on them l doubt water could get in there. Do you have an inline fuel filter, and original vacuum operated petcock? Open the fuel cap to see how it runs. Mabe a clogged air vent in the tank and the rain was coincidental? If you have good sparks it must be fuel related.

 

You can also check for vacuum leaks around the carburettors with some butane gas or starter fluid. If the bike was running properly before the downpour its unlikely its carburettor related.

 

I actually don’t have an inline fuel filter, which means it’s possible some junk got into one or more of the mini filters inside the carbs. But I don’t think it’s the fuel cap air vent, since I was running the bike off the aux tank and still having issues. I also do have an original petcock, but I rebuilt it and have verified good fuel flow under vacuum.

Starter fluid is probably also a good idea to try. I don’t have any of the classic symptoms of a vacuum leak, but my intake boots do seem to have some surface-level cracking. You can see it in this picture I took when I was taking the carbs off to replace the throttle shaft seals.

 

If necessary you can repair them with inner bicycle tubing and RTV. But it's not going to develop vacuum leaks suddenly especially on more that one cylinder. Even though you can see sparks with your colour tune it can still be missing intermittently. Just to eliminate this l would check the aforementioned wiring and alternator output just to be certain.

 

Mine too. I ended up baking the coils in a low-temp oven overnight, then sealing them with a coat of varnish. I eventually threw those coils out and fitted Honda's finest.
For the HT leads I encased them in electrical sleeving (the corrugated kind) and carefully taped over the ends at the plugs, to make sure nothing got in.

 

Good idea with the electrical sleeving I might try that on my bike.

 

Alright, so I have a bit of an update. Sprayed carb cleaner at the intake boots while running, no change whatsoever. Looks like I don’t have a vacuum leak. The bike still weirdly appears to run better at higher RPM, like it smooths out over 3000. Problem with switching over to the alternator from the battery, perhaps?

Also disconnected the TCI electrical connectors and sprayed contact cleaner in there, no change. I see the connection from the voltage regulator to the alternator, but I’m not sure how to disconnect that one without removing a bunch of stuff that’s in the way. I tried spraying contact cleaner through it from the top, no effect.

Two questions now, since I’m a noob at troubleshooting electrical problems. When I check the alternator voltage, where do I do that, on the battery leads? Second question: where exactly is the pick-up coil? I can follow the wire partway from the TCI, but it sort of disappears under the bike and I have no idea where to look for its connection.

 

Yes, on the battery - look for 14.5 +/-.3VDC at approximately 2000 rpm and up with a fully charged battery.

Pickup coils are under the left crankcase cover and the wiring terminates in the plug that attaches to the TCI, so no connectors along the way to cause trouble.

 

You can wait until you check voltages but this connector is notorious for a poor enough connection to cause overheating to the point of melting the connector