Bike won't start

Ok, so I'm nearing my wits end.
I have a 2010 Yamaha WR250R. Full exhaust, fmf programmer, and gears. I recently washed the bike and ever since then the bike hasn't cold started.

The bike will not cold start at all but will crank all day, if I push start the bike it starts right up but if I don't let it warm up it will stall. Once I let the bike warm up, I can turn it off or let go of the throttle and it will idle just fine as I adjusted the idle, but the second I go to start it up it will crank crank crank and when I twist the throttle all the way then it will start sometimes but still after hesitation.

I really can't start the bike without twisting the throttle but after the spark plug install I noticed I can get away with it sometimes when it's super warm by just pushing the start button.

I have replaced the battery with a brand new ytz7s 130cca battery
I have replaced the spark plug with a brand new cr9e spark plug
I have put brand new premium fuel in the gas tank
I have cleaned and opened any airways that may have been obstructed

Only thing I have left to try is to remove the fmf programmer cause maybe it shorted when I was washing the bike...Other than that, I am at a complete loss.

Any suggestions would be amazingly appreciated! HELP!

How many miles on the bike?

Have you checked the valve clearances?  

Tight valves lower the engine compression which will cause hard starting.  On carb bikes usually you can get it to light off when you choke the bike but it won't idle unless you crank up the idle speed.  Then once it is warmed up the idle is racing too fast and you need to turn it down.  Not sure how this plays out with FI.