99 yz400f problems

I have owned a 99 yz400 for a few months now. I accidentally dropped it in a mud hole while riding. I made the mistake of running to get it to my truck to take it home. It ran perfect for several weeks, then... I noticed a rattling in the top end and it didn't want to stay at idle. I discovered there was water in the oil, so i flushed it several times with diesel fuel and oil. The majority of the water is gone, but the problem still exist. Any advice?

So you let oil mixed with a lot of water/silt sit in your bike for several weeks and rode it during that time? Only advice I have is to take it apart and see whats wrong. And get a manual if you dont have one.

what is the best manual to get? yamaha, clymer, or something else

Yamaha.

they have them for free here. search around a bit.

thank you for your advice, but i was trying to get an idea what to check or possible problems to cause these issues. I guess I'll have to get the manual and check everything. I really just wanting to know if its carb related or if its something internal or what.

You had muddy water in your engine oil. Time to tear the engine down and flush out the tank in the frame.

Change your oil filter too. It's probably full of dirt and whatnot right now. Since the sound is coming from the top end, the first step would be to take off the head cover and go from there.

thank you for the advice, i just got the oil flushed and changed the filter, im gonna clean the carb and see what happens. I'm trying to avoid going in the bottom end. Everything in the top end seems good. Im hoping its just water and or dirt in the carb. Ill keep everyone posted.

If theres a rattling in the top end i doubt it's a carb problem.

i tried running it off straight starter fluid and it ran perfect, no noise or anything. Does this mean it's just a carb issue?

That's usually a good clue, yes.

I'm stumped, my guess is carb problem. I'm guessing Gray has useful advice, as usual haha

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