Water in 1993 Engine during bad rain storms, clutch not engaged

[92GS500Lv]

Sad story,

1993 working great for years.  recently left out in the rain during the worse July storms.   Seems like water made it in from carb inlet , cant see how else.   Unknown issues so started the engine to ride.  Oil over flow as engine heated up.  Also the clutch lever would not push out the clutch.  Cable and rod looks like they are moving.
Turned engine off,
Drained oil/water mix.

Sitting wondering what to do next.  Remove clutch cover?  restack clutch?  reassemble with fresh oil and filter?
Restart engine let run and drain oil?   
Seems like the engine is working,  but not sure hot to get past this water issue and minimize long term issues.

Experts at this please respond. 
Keeping the motorcycle indoors as it was for five years and not exposing to rain again if it can be helped.

Tyvm

Fingers crossed.You cannot view this attachment.

[Armandorf]

Winterize next time, use a cover for the bike.

Now to clear the clutch plates I would leave the clutch lever engaged with something like a rope or string. Rotate the engine.
And do two oil changes in a short period to flush it.

You can also use some additives to engine flush.

I went the savage way by directly pouring gas in the block and cranked it by hand. The problem is that you can ruin rubber parts. Kerosen is better in that regard but I wouldn't recommend it either.
If after that cheap flush a seal starts to leak you would be thinking why you didn't just change the oil twice.

Lastly I hope you didn't scratch the bearings with the oil water mix, I suppose that if you change it soon enough and don't put a ton of load in the engine it will be fine.
How long did you ride it like that?

[92GS500Lv]

It ran for less than five minutes.  The clutch engaged but did not return.  The rod is pushed in but did not return.  I am taking the clutch basket out tomorrow to inspect it. 
I will be flushing the engine twice.  I guess twice the filter would be appropriate too.  they are only $7

[Bluesmudge]

The bike should be able to sit through any rain without water getting into the engine. Are you 100% sure it is water and not gasoline? I don't see how water gets into the engine unless it's leaking into the air box in large quantities somehow while an intake valve is open.
Was there water in the air box or carb bowls?

[Armandorf]

The bike should be able to sit through any rain without water getting into the engine. Are you 100% sure it is water and not gasoline? I don't see how water gets into the engine unless it's leaking into the air box in large quantities somehow while an intake valve is open.
Was there water in the air box or carb bowls?

yes, good point.
i would also check the tank drain hole, maybe fitting a guitar string or pouring hot water to see if camse from the bottom.
Gas tank hole recession could fill with water and ends up in the gas.

[92GS500Lv]

It is fuel contamination.  When I drained the oil it was not cloudy and smelled like gas.  The fuel tank had less gas in it than I remember when I last filled it.  Not sure if the fuel vale failed.
I emptied everything.  Fresh oil and filter.  Ran engine for two minutes.  Seems to be working fine.  Draining the oil gain for a second flush and replacing the filter just in case. Looking online for a new fuel valve.  I disconnected the fuel line to the carbs and no matter what setting I put the valve in : Prime, reserve, On.  fuel still flows.  I have it pinched off with a clamp for over night storage. 
1993 might be more than past replacement time. Also ordered new clutch friction plates.  They seemed very thin show signs of heat issue. 
Ty.

[Bluesmudge]

Fuel in the oil usually requires two things to fail: the petcock (fuel valve) and at least one of the two carb float bowl needle valves. If both needle valves were closed and working correctly it will stop the flow of fuel into the engine., even if the fuel valve send fuel 100% of the time.

I would replace the petcock and both float needles. Might as well for reshen up all the rubber bits/Gaskets and clean the carbs while you have the carbs disassembled to get to the float needle valve. With the float needles, be sure to go OEM. I've been burned by bad aftermarket carb parts causing similar issues to what you have.

Also check your tank for rust and see what the condition of the petcock fuel screen in. Stuck float valve is usually caused by debris in the fuel. Usually rust in the tank. But could also just be so old and worn it's not sealing well.

Did you measure the thickness of your clutch plates. There is a spec in the repair manuals. After 55k miles my plates are still well within spec but I had to replace the clutch springs.