Starts but wont run

Have a 2007 400 fis that sat for over a year. Put a new battery in it. it turns over and starts if you prime it but then quits. i cleaned out the bottom end of the carb, cleaned out a jet that was plugged up  but no change. starts run for a few seconds then dies. any ideas???  

The fuel system is still dirty/clogged somewhere.  A complete tear down of each part and cleaning is the only way to know that fuel is getting into the carburetor and into the engine properly.  There are lots of small passages that clog over time.  Typically "dipping" is the only sure way to clean these passages.  

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junkman is right...sounds like you need to dip it carefully... however dipping wont always clean thew jets. the jets are small and the amount of fuel or debris needed to clog them up is very small. i suggest using a torch tip cleaner or a .10 guitar string to push through them as well.  but lets also look at the fuel petcock.  usually with the main jet being larger with the needle running into it it doesn't clog. so even with the smaller pilot jet clogged they will usually run via the main jet if given throttle.  so based on your description it sounds as though it wont run at all without priming and dies out once it burns the primed fuel.  

they way fuel enters the system is pretty simple. through the tanks petcock (on off valve) to the fuel pump (which reminds me....check the hoses going to and coming from the fuel pump...if they are cracked and rotted they can lose fuel pressure and still not leak..could cause this problem as well) from the fuel pump the fuel enters the bowl of the carburetor via the float valve. the pilot jet siphons fuel from the bowl for idling.... the main jet siphons fuel into the carburetors plenum when you give it throttle...(the throttle cable raises the needle)  and compression sucks the fuel from the carburetors plenum into the cylinder...  so it really sounds like you have either debris and gummed up fuel in the fuel petcock, or the fuel pump is having issues...  
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Hello,
 It does sound like a carb problem. First check your petcock and filter for dirt or debris.
 I suspect dirty, clogged, restricted jets and passages and even a sticking or dirty needle and seat asssembly. Also check for vacuum leaks and rotted rubber fittings such as your carb mounting flange.
 I would completely dis-assemble the carb and soak it in a very good quality carb cleaner over night. Soak it in very hot water to get the carb cleaner out. Thoroughly blow out ALL the passeges including your slow speed jet and accelorator pump passage. Assemble very carefully setting your float to specs (usually closed at the level position).
 One thing I like to do is devote a set of screwdrivers, pliers, and small crescent wrench to the exclusive service of carburetors. I work on a lot of stuff and have usually had to grind, file, or notch a screwdriver to make it work effectively. Even though it may seem destructive I still do this to really good quality screwdrivers. They usually don't break or bend under the sometimes needed pressure associated with removing jets.
 Another thing is a good workbech with borders so that parts don't roll off it. A metal tray is good too.
Good luck.