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I've had this bike about a month and a half, and everything has been peachy until about a week ago.

The bike has started missing under acceleration, and now has gotten to the point where anything above ~5% throttle is causing it to sound and ride like it's running on two cylinders. Sometimes it clears up and runs beautifully for a minute or so, then returns to running horribly.

Cold startup is fine, it fires right up and rarely needs the choke, but after warmup, I can't get the bike started from a stop without it stalling. Trying to accelerate from a stop usually results in the bike bogging and again, dropping to what sounds like two cylinders. I have yet to pull the spark plugs (they were replaced ~500 miles before I bought the bike), but a fresh tank of fuel and a little bit (~0.5oz to 1oz) of Lucas fuel treatment hasn't cleared the problem up yet.

Where should I start looking?

Id check the plugs. depending on how the tank is (old gas at some point?) also could have run rich at one point. not a big deal to replace them.

I would start by pulling the plugs and reading them. Keep track of which plug comes out of which hole. See if any of the plugs are burning differently from the others, that will tell you which cylinders are involved. It could be a plug or plug wire breaking down and causing it to bogg. If you have a couple of plugs that are sooted up, you may only be into cleaning or replacing the plugs. The problem could be as simple as water in your gas which is fouling your plugs and clogging the jets. You should be able to get some insite into whats going on once you have a look at the plugs. If you suspect water in the gas [ which I do ], drain some of the gas from the carb bowls into a clean glass container, you will see water laying at the bottom on the container. Gas and spark plugs are the two areas I would look at first. Xs

Well, I believe I've found my problem. We started by checking the plug wires, and pulling off the wire on the #4 (leftmost looking at the front of the bike) cylinder was causing the wire itself to arc (along the insulated portion of the connector) to the head. I'm thinking the wires are bad. Any reason not to believe this?

On a 13 year old bike? I'd believe that . If the wires are not molded into the coils, it should be an easy fix. XS

xsyamahadg wrote:On a 13 year old bike? I'd believe that . If the wires are not molded into the coils, it should be an easy fix. XS

They are.

Accel makes an upgraded universal coil set I'm thinking about going with, rather than the stock Yamaha units, for the simple fact that the Accel wires aren't integrated into the coils.

It's still going to cost me $160, though.

Good thinking, the Accel units will be about half the price of Yamaha. Get yellow wires, that's my favorite color.

Caught an amazingly lucky break... decided to replace the plugs (all four looked normal except for the one cylinder that was missing having some residual fuel on it) as a first step to troubleshooting. The plug from the bad cylinder basically fell apart in my hands. The threaded tip that the plug wire attaches to had at some point (the bike had been dropped once, I think it was knocked over in the hangar the previous owner kept it in) gotten bent, and was barely hanging on for dear life. I used a pair of pliers to twist it off, and discovered that about 1/4 of the electrode was the only thing holding it together.

So $10 and a fresh set of NGK CR8Es later, she runs like a champ. Idles steady as a rock and pulls much better. I imagine fuel economy will improve somewhat as well.

I'm still planning on replacing the coils/wires though, as that arcing does bug me. I'm probably going to go with the Accel coils and black wires, as the whole bike will be getting disassembled and reshot in either flat/satin black or BMW diamondschwarz (a black with silver flake in it, looks silver in the sunlight) before too long.