Im told that the breather on the 06 yz250f can **** water through the engine if you stall in water, how do you overcome this problem?

So it's not the head gasket? And you are still losing coolant? Well, okay, you will have to find how the water is getting into the rocker, and whether it's your lost coolant or plain water. IDK, possibly an intake manifold leak?
Even though the oil looks clean, the water and gunge in the rocker area will drain into the sump and contaminate the oil. If it's not the coolant, run the engine until it is hot, then give it a few minutes for the oil and water to drain down from top of the engine into the oil sump. Then change the oil and oil filter. Good luck, hope you find the problem.

Try running some fuel system cleaner through it. A good choice is Chem Tools Berryman B-12. There are some hardworking solvents in the product that could help you overcome a dirty carburetor. Initially use a good, strong dose. Maybe double what they recommend . (1 oz/gallon). If this doesn't work, the carb will probably need to be removed and inspected and cleaned.

on the inlet manifold is a breather from the engine i think on this year so check for a split vacumn hose or a split breather pipe ,failing which it could be the thingy on the back end of the butterfly ,their is a sensor but iam pretty sure its a breather pipe or something stupid ,also pull the vac pipe out of the servo and just try pùtting a plug into pipe in case the servo diaphram has split

Tell me when you fill up how far do you go before it stops,,then how far does it go the second time and the 3rd time ,,Do the times get longer each time,, if so then your problem isent a big deal.
The problem you might have is that the return fuel pipe from the engine returning fuel back in to the tank,, and the TANK breather pipe which has to let air in as you cannot take fuel out and not let air back in ,,so it causes a vacuum in the tank... So check the breather before any thing else .. OR dont fill it up any more than the first click of the pumps .
Let me know how you get on Ron