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94 cr250 water in gearbox

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I recently bought a 94 cr250 with water in the gearbox. I was told it probably needed a new cylinder. It seems that when this happens the most usual cause is the water pump, so I snagged it cheap thinking it would be a cheap fix. I took the water pump apart and didnt see anything wrong with it. It had good seals, and there were no grooves in the shaft. There were shiny spots where the seals run, but they passed the fingernail snag test with flying colors. So I put it all back together. I left the drain plug out of the gearbox and started filling the radiators with water, and it was pouring straight through the motor and onto the ground. Where should i look next?

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Well, it would be the water pump seals, or else the right hand crank seal is so bad and the head gasket are bad, that the water is pouring through the engine into the gear box.

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ok, yesterday water was pouring straight through the radiator, into the gearbox, and onto the ground. so I was pretty sure it wasnt a small crack that opened up when the engine warmed up. I was looking for a hole. I took the cylinder off today, and the base gasket was missing a small portion, between the water port and the power valve linkage. with the cylinder off, i filled the crankcase portion of the water jackets with water, and it held. no leaks there. I plugged the two water jacket ports in the bottom of the cylinder with my fingers and poured water into the inlet/outlet on the head, and it held water. no leaks there. It must be the hole in the gasket letting water into the power valve linkage and therefore into the gearbox. does that make sense to anyone but me???

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so....I almost got this thing put back together (engine complete except for the carb), when for some stupid reason I spun the rear tire to find TDC. My piston is hitting the head. F******k. Apparently at some point in time, a previous owner upgraded the piston and head to a 97 and newer flat-top style. My new 94 model domed piston isnt working. I dont want to tear this thing back apart. Are there any options other than a new head, or lots of head work? Anyone want to swap for a newer head? Its a little beat-up, but not bad.

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