WR dead after FMF install! Please help me.

Hello everyone and thanks for looking at this. After a lot of years of mainly street riding, I traded an Aprillia RSV for an almost new 2009 WR250R.I love this bike!! SO much fun. But after getting a little tired of the lack of power everyone else seems to notice, I bought and installed an FMF exhaust system, a 12:00 labs exhaust emulator, and and FMF Power Programmer. All installed nice and easy, and when I fired up the bike, it seemed great. A little noisier but I kind of expected that. I started inputting the settings I found off the net that worked for everyone else, and before I got done the bike shut off.
I tried to restart it to no avail. It wouldn't even crank when I hit the button. I plugged the stock FI plug back in where it should go and still nothing. I thought maybe I drained the battery out from running it at idle during programming so I threw a battery tender on it just to be sure. The battery is near new, BTW.
I returned home tonight, turned the key, and the bike fired up perfectly. I finished programming it and rode it one block up the hill. A little hesitation right off idle if I crack the throttle but that was it. I turned around to ride the one block back home and as soon as I got there the bike died again.
No cranking, nothing.
When I turn the key on, I hear the fuel pump prime like normal, the far left green LED on the programmer comes on for about 2 seconds, shuts off, and then the far left LED comes on.
Then a relay clicks rearward of the battery and the whole thing shuts off. FI, starting circuit, all I have is the display on the dashboard.
It seems if I let it sit for a few hours it will start again but the same thing happens, it shuts off after a few brief joy filled minutes.
I would really appreciate it if anyone could guide me in the right direction on fixing this. SO far nothing from FMF (whose programmer website seems to be inoperative for contact purposes) or Dobek, but it's been a big holiday weekend so maybe next week. As for modifications to the bike, it was basically stock and in beautiful shape with the exception of the programmer, the exhaust and emulator, and I have removed the airbox flapper and the little solenoid that had the vacuum lines. Yes, I plugged the lines.
Thank you all and I hope to have some good experiences to share soon.

Sounds like a clutch or sidestand switch issue, or a loose wire somewhere with the starter.

I don't think it's any of those. I wondered the same thing but I have had no issues until I put the programmer on. And it seems to act like it needs to cool down even though I have not even warmed it up yet. After a while (I tried again this morning) the bike will fire up immediately and then die within a minute or two.
And yes, it has fuel. I know someone's going to ask me that.
I can try bypassing them later when I get home from work.
Any other thoughts?

If all lights are coming on but you aren't getting any crank, then it is not a fuel issue, it is electrical. I still think you probably bumped or manipulated one of the harnesses so it is loose somewhere and giving an intermittent open circuit. I just can't tell you which one...

HA!!!!! HAHAHAHA!!! I finally figured it out. Seems for some reason, maybe it was there before but I never noticed because I don't really make it a habit to run my bikes while they are on the kickstand, but once this thing warms up, there seems to be some interplay between the clutch lever, the neutral sensor, and the kickstand. I tore the bike apart, looked over everything, and thought I'd see if maybe the lean sensor was defective. I stood it up, it still wouldn't start, and then for some strange reason I put the kickstand up.
Bingo.
The switch is functioning perfectly, but I need to have the clutch lever pulled in. Also, I now notice when it's warmed up the neutral light doesn't work even though the bike is in neutral. SO basically, once the bike warms up, the neutral indicator quits working which tells the bike that it's in gear and if the sidestand is down and I don't have the clutch pulled in, it will die.
Crazy, right?
Anyway, Matt from Dobeck was awesome and I thank him for all his head scratching. Now, I'm gonna go program the thing, get on it, and annoy my neighbors.
Thank you all and I will post pics soon!

You connected the programmer to the battery?
You did the vacuum delete when you removed the EXUP?
You can disconnect the clutch switch (just unplug it and tuck it in around the headlight).
Is the kickstand sensor damaged?