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I would inspect the head for warpage per Yamaha's directions. If out of spec, you could have a few thou removed. In which case you might want to consider the use of a slightly thicker gasket.

I am not understanding your comment about the flywheel not being threaded for this installation of the puller assy bolts.

When you say that it "seems to be" the charge coil, what do you mean? You should be able to test the charge coil in situ to see if it is within specifications or not.

It is conventionally threaded. To loosen turn counter clockwise. Flywheel is tapered. You will need a puller to remove it. If you think the nut is tough to loosen, wait until you try to remove the flywheel.

Thanks for the feedback. Glad to hear that you got it up and working.

The tachometer works on frequency. AC frequency. All three green leads have the same frequency.

Absolutely systems need to be topped off with hydraulic fluid from time to time. I would start there.

You can always tap into one of the three green wires to get a signal for the tachometer.

What has Yamaha said?

Clogged carburetor may be the reason for no fuel to the number three cylinder. Mist some gasoline into the throat of the carburetor and see if that cylinder starts working. A failed diaphragm on the fuel pump can allow gasoline to get into the crank case.

What kind of thoughts? Thoughts related to water in the oil? My first guess would be a failed gasket. Now where is the water? Just in the lower cowling? Just in the oil pan? Or both?

I would guess a chafed wire issue. Up trim wire chafed to the starter motor relay wire. Why not check the two wires for continuity to each other?

1998 200 what? There are multiple 1998 200 models. Why not use the Yamaha parts catalog to find a Yamaha part? Novel concept that. I will make a guess.

Is your question about no fuel to the number 3 cylinder or is it about gasoline pooling in the crankcase?

Removed the oil injection pump temporarily or permanently? Why?

I thought you said that downloaded the service manual?

With a digital meter, when taking ohm readings, hold the probes together. Note the resistance seen. Say it is 0.2 ohms. Subtract this value from the resistance seen when testing the resistance of a component.