Water in oil where do I start?

Hello guys I just put this motor together all yz426 parts from various bikes and I go to put a brand new timing chain in and all the water from rad was in oil. So I took the head off and it wasn't warped. I took water cover off anf its covered in rust could the bearing and seal be bad? Any sugestions on where to go from here would be awesome!!

The water pump can't leak into the engine because the oil and coolant seals are separated by an air gap leading to a port under the pump that drains away any leakage. 


There's an O-ring at the right crankcase cover behind the pump, one at the front of the cylinder base, and there's the head gasket.  Those are the only sealing elements that could cause contamination, other than cracks in the head, cylinder, crankcase, or RH crankcase cover.

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