I just did a head replacement on a 99 flex fuel 3.0. I got it all back together and started it up and it ran kind of rough on the first start up and sounded like it was backfiring through a cylinder so I shut it off. No funny smoke or anything other than missing some. I turned it off and it hasn't started since. I pulled the plugs out and they were black and wet. Gas flooded I assume. While I had everything apart I replace the fuel injectors seals and put new plugs. I cannot get it to start back up I have no CEL I guess because I only ran the engine for a couple of minutes. I went back and double checked all electrical connections and vacuum lines. I have took the plugs and cleaned them and as soon as the weather breaks I am going to try it again. My big question is why did it start the 1st time and not restart after the initial start instead flood. Do I need to let it run long enough for the thermostat to open and start circulate the coolant, and what would cause the backfiring sound through the engine? BTW when I tried to start it again it sounded like it was trying to start but never would. I unpluged the harness to the coil pack to see if it would turn over smooth without any fire to see if I could detect something mechanical and everything was smooth. Any help here would be appreciated !

 

Double check, then triple check, the coil firing order, I still get it wrong after 35 years.

All fuel injected computers have a program to clear a flooded engine.
You turn key on
Press gas pedal to the floor and hold it there
Crank engine

Engine should now be turning over with spark but fuel injectors are shut off.
TPS(throttle position sensor) outputting maximum voltage(4.5v, foot to the floor) before cranking "tells" the computer to shut off fuel injectors.

What I would do is to pick an easy to get to spark plug, remove it and clean and dry it, then re-install it.
Now crank engine as described above, with injectors off.
Do it a few times, if engine tries to start then it is getting fuel and shouldn't be, so there is a problem, see below.
Pull that spark plug back out and check it for fuel, if it is wet then you have a leaking injector, or a bad Pulse Damper.
Pulse Damper is at the end of the fuel rail and will have a vacuum line attached, pull off the vacuum line and check it for fuel or fuel smell, if there is fuel or smell then it has a hole in the diaphragm and needs to be replaced.
If no smell then leaking injector.

The Fuel injectors all get 12volts when key is on, the computer opens an injector by Grounding it, there is one ground wire for each injector running back to the computer, so 6 ground wires on a V6, if one of these wires gets chaffed and gets grounded then that injector would be open whenever the key is on.

 

Thanks ! went back and double check the coil firing order and it was off on the drivers side. Started it up and everything was good to go. I really felt like a real idiot even after checking and found what I found. Thanks Again !