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If you had water in the fuel you would have water in all of the cylinders. However, for it to be still sitting in the cylinders I doubt that the motor would have run with that much moister. My motor ran fine in the driveway with muffs on with the blown head gasket. It is only when under load that you can obviously tell if something is wrong. However since you said it was running on a hose in the driveway I can now understand way there would still be moisture in the cylinder. The motor probably never got hot enough to get rid of it.

Cost of rebuild has a lot to do with how damaged the block is and also if it is a freshwater or saltwater motor. My motor is a freshwater only motor so it dismantled very quickly and easily. Heavily used saltwater motors tend to be a lot motor work due to seized and deteriorating, nuts, bolts, and other fittings. Next, once apart what need to be fixed or replaced. Are the cylinder walls scuffed or scored? Can they be just honed and saved or do they have to be overbored and hope for the best. New pistons, bearing, rings? How much are you willing to do yourself?

With my motor I derigged the powerhead myself and took it to my mechanic. He was able to save the cylinder through rehoning it (had him do all of the others was well), I had him replace all of the pistons and they all got new rings. All new bearings from the crank to the wrist pins, all new gaskets through the entire motor, all new thermostats, and he rebuilt the carbs. I brought the motor and boat back to him where he reinstalled the powerhead and rigged it back up. I was at $2500 when finished.