Water in the tranny is not caused by o-rings on the head. You do not need to split the cases to rebuild the water pump. It would be the oil seal behind the water pump shaft bearing. It is right next to the mechanical seal. #14 If it was the mechanical seal there would be fluid coming out the weep hole.
(http://www.servicehonda.com/hard%20parts/atv/trx250r%2086-89/water_pump.jpg)