Help with a dreaded and head scratching problem

Well I'm looking for help and I've tried to fix a huge problem so if anybody has some advice please throw it out there. So the story goes like this. About a year ago me and a bud just installed a new winch on his 06 jeep rubicon and took it upon ourselves to go out into east Texas to go shooting. My friend being from Utah laughs at the lack of Moab style off roading where we are at. And i explain to him the classic texas style of mudding. And to look into a snorkel. Well he laughs and says he won't be doing any of that and we carry on down the trail. Well a hairpin turn comes up and and we do a nice fishtail around the turn and there it is a sweet mud puddle that called his name out. Thinking it was smaller then it looked he decided to plow threw it. And at the last minute realized it was longer then we expected so tried to back out but mud carried us all the way to the puddle.  Now stuck, what better way to break in that new winch. So he attempts to winch his self out of this massive puddle and me being the great friend decided to take pictures cause I was not jumping into that water. Well after some attempts to get through the water/ mud, a thing called suction left my friends jeep at 70 degree angle leaving the passenger side completely underwater. So there is the back story to get the brain thinking about what it went through, here is the problem.

We have attempted to get this vehicle running and so far no dice. We have drained oil, replaced plugs, replaced relays and fuses. Changed air filter. Everything we have done thus far we have failed to get the jeep to crank. We are about to replace the ecu. But starting from step one what should we check recheck and check again to get this vehicle started. And what preventative maintenance should we do to to get it back to a trail rated state.

Here is the condition as it sits

No crank
No start
Has power to turn on lights and radio and aux compents
Check engine light is on and flashes, which i believe is a critical fault  

`hahaha well i have no idea what to help you with sorry but great story! it just proves my theory on newer vehicles and electronic stuff  are crazy wen wet!!  i keep it oldskool less to worry bout good luck  
noise mud exhaust fumes!

The OBD2 scan tool will be your best friend in this situation. Plug it in and it will tell you what is wrong and then you get to fix it......simple. Good luck, nice story, do it again sometime...lol.  

Take it to an Auto Zone and have em hook it up to their "computer", its FREE and will tell you what sensors/electrical problems are bad.  I think that the check engine lite blinking has something to do with a sensor so they should be able to point you in the right direction. GOOD LUCK and tell him next time to test the holes depth with a stick b4 hittin it....LoL  
My bumper sticker says "NOT A HIPPIE JUST A WELL GROOMED MOUNTAIN MAN" LoL