RE: s200TXRU Yamaha flat spot/ hesitation
That 1996 motor usually performs better if it is propped closer to 5500 rpm. I'll bet a one size change in prop pitch (smaller) would make a world of difference.
Because the S200 has different tuning specs than the other 200 models that year, perhaps the WOT timing is set wrong, 21° vs. 20° for the regular 200. There may be a throttle linkage adjustment that is not correct also. If the diaphragm fuel pumps haven't been changed in a number of years, go ahead and do that automatically just to be on the safe side. There is a chance that carburetor cleaning may be needed, but I kinda doubt that from your description on how the well the motor runs otherwise.
It might be a good idea to have a Yamaha trained technician check over the motor completely, paying close attention to the adjustments and the condition of the fuel system. Of course a compression test should be done first to see how the internal condition of the motor is.
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