WR250X dies at idle

Bought my son a 2008 WR205X, I have a 2005 WR450F and he wanted to try supermoto, so I figured I would buy some SM wheels and tires and we could do it together.
Bike came with an FMF slip on, stock header pipe & FMF controller, still has the smog stuff and stock airbox with flap door,  looked like it was new, great condition.
It needed a new battery when I bought it, so replaced that, and it ran fine for a couple of weeks, recently it started running rough and would start & idle but as soon as you give any throttle at all, it dies.  After some research, I dumped the fuel tank & filled it with no ethanol premium (no change)  I removed the FMF controller,  replaced the spark plug, (no change), the spark plug boot/coil was really rusty, so I replaced that (no change), read about the fuel pump issues, replaced that, (no change) after replacing the fuel pump I noticed if I held a shop rag on the end of the exhaust pipe to create backpressure, it would run, not well, but it would not die.  I have worked on carb bikes for years, but never EFI, so now all I know to do next is take it in to the dealer.  K&N Yamaha, Tulsa Ok,  great people, Norm McDonald was the N in K&N before his partner started making aircleaners.
Oh, I also checked the plug on the front next to the radiator shroud that people say can get loose.
When I can get it to run, it bogs like it is not getting fuel, when twisting the throttle you can feel how its not running, then it will kick in, but rough as hell.
Ideas?

maybe your idle throttle is to low..

I will try that tonight, thanks.

Did you lift or play with the gas tank while putting on your upgrades by any chance?

Has the fuel pump been replaced, 08 its a common problem, they start to fail slow then you will have nothing.

I had a 2008. The fuel pump problem never showed up on mine even though I've read that it is a common problem for that year.

I did, however, kill the pump myself. When I upgraded, I took the tank off and when i put it back on, there was a kink in the fuel line. Usually, these things are easily avoidable, but with the WR, I put the tank back on with a kinked line because it honestly looked fine. I did the same thing with my friend's WR. I only noticed it after both he and us started having fuel pump issues, which I thought was an odd coincidence and hence why I took a second look.

I would suggest making sure the fuel line is well placed. I made the mistake twice and I'm quite used to playing around with bikes, so I'm sure it can happen to anyone.

how many miles do the valves need adjustment

at 10000 miles mine needed adjustment if he bought it used there is no telling how it was used

Replaced fuel pump assembly, runs like new.

My 09 is doing something similar, except it dies at idle. When stopped waiting for a green light, I have to continually blip the throttle to keep it from stalling, and if it does stall, then it starts up with difficulty. ( have to vary the throttle position till I find a spot where it starts ) I am getting some backfire, black carbon around the exhaust exit on my fmf powercore 4, smells like unburnt fuel mixed in with the exhaust gasses. It has the airbox mod,( door removed ) ais has been deleted, K&n air filter. Also has an fmf programmer and stock header. My first step that I'm trying is fresh fuel treated with a heavy dose of sea foam. I am hopeful but not optomistic that this will clear it up. On heavy throttle the problem is not evident, so that makes me think the fuel pump is ok???  Any suggestions are appreciated. Rubber side down, Dave