I have an 07 and had the same thing happen when I first purchased the bike. It sat for at least 6 months before I picked it up.
Seafoam will be your best friend. I poured a few ounces of it in my tank and topped it off with fuel, rode 20-30 minutes (where it would have to be fully choked to run) and it magically came back to life. Runs fine now. It does wonders, but doesn't do what a brush and elbow grease will do.
Try to start your bike choked, (I typically start it, and while it's warming up is when I put my helmet and gloves on, giving it a minute or so to warm). Leave the choke on and take off. Don't ride it hard, just ride it. When the needle gets above the first line on the temp gauge, kill the choke.
If it still stalls, you need carb work.
If you haven't been referred to this page, it's your lifeline. Everything you'd possibly need to know about the 250 you'll learn here.
Ninja250 Howto - Ninja250Wiki
Good luck man.