Ok everyone, so here's what's up.
My 98 CBR got stolen in october and whoever stole it was nice enough to crash it and abandon it so I could pay outrageous impound fees to get it back. They told me it was in decent shape, so i went and got it and brought it back to my place. The frame is in great shape, and the bike started at the impound, and quickly died. So, we need to get it running before I tell you about the other problems.
The tank was open, so i assumed since the tank was about half full it had lots of water in it. I took the tank off, drained it and let it dry out a few days. I put it back on today and put some fresh fuel in it. She is turning over fine and wants to start. IT STARTS! here's where i run into a problem. It starts and blows about a gallon of brown (dirty, not oily or gas) water out of the exhaust and then dies again. It was running for about 10 seconds. Then, I couldn't get it started again, but it's still turning over.

the oil is fresh and the plugs are nice. Anyone have any suggestions?

 

Sounds like moisture might have gotten into the cumbustion chamber. I would take out the pluges and spray some lube(not WD-40) in there. Then turn the bike over for a little about 10 seconds. Clean out what you can from the cylinders. Spray some more lube into the cylinders. Then turn over for 10 to 15 seconds and again clean up what was pumped out. You'll have to repeat this many times and quit when the "brown" water stops coming out of the engine. Then put in a new pair of plugs and change the fuel filter. Also, make sure the inside of your tank isn't nothing but a pool of rust. From the sounds of it, your tank would most likely have rust in it. I had a jet ski engine that was FULL of lake water and this is what I did to get the water outa the engine. Took about 4 hours of cranking and cleaning up the mess before I had all the water out of it. Funny thing is that it's been 7 years since that happened and the thing still runs like a raped ape.

 

Along with those ideas, I'd lift the front of the bike up as far as you can, or remove the exhaust, there could be water sitting in the bottom of the exhaust pipe between the engine and the exhaust.

 

Bet it sat on it's side for a long time and there's a bunch of oil that made it's way above the pistons. I'd first change the plugs and see if she runs better.

 

Actually the plugs look fine, and as far as i know there isn't oil in there. The police recovered it standing up on it's kickstand. Whoever stole/crashed it picked it back up.

 

If there was oil above the pistons in the cylinders, then the engine would hydro-lock the first time that piston tried to come up on compression, if there was enough oil in the cylinder. If it ran, even for a short time, I doubt there's much oil above the pistons. Any oil that might have gotten above the cylinder head would have drained back down to the oilpanas soon as it was stood up. Getting water out of the exhaust would simply be removing the entire exhaust system from the bike and standing it up on it's end. It's easy to get off and simple to do. I'd be concerned about water in the fuel lines or gas tank. Removing both the tank and carbs for a good cleaning is probably a good idea. I'd also do a compression test to make sure you don't have a blown head gasket. If they were riding it like they stole it, then you could have internal damage. A compression test would help to determine problems with head gaskets, piston rings, the valve train, and valve guides. Good luck and let us know what kinds of things you find during your work on it.

 

I'm gonna pull the exhaust and replace the plugs and check compression tomorrow. Thanks guys, for everything.

Also, I broke my finger on sunday so I'm doing all this in a splint. Things are hard enough to reach on this bike as it is!