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We have an e250 5.4liter v8.  Yesterday we ran through some standing water now the engine misfires and the check engine light is on.  

the spark plug tubes are filled with water....

you will need to blow them out with compressed air..

using a LONG tube ended air nozzle..  

the coils will need to come out also...  

so you can blow all the water out..

you did not post a year...  

i have found a LOT of 5.4 motors with vacuum elbows that have collapsed.. and are leaking..

there are probably several other things that are water logged...

you really .. if you have a shop.. want to blow out everything with compressed air..

use a leaf blower to start.. if you don't have compressed air..

you will also probably need to remove the complete air filter and tubes all the way to the throttle body.. to verify they are clear of water.. and the filter is not damaged..

there is usually an inlet air temp sensor that really does not like to swim in water...

there is a chance that the motor injested water... this would not be the first time..

it can break the pistons.. BEND the rods.. blow the head gaskets.. .. lift the heads off the block..

since you did not mention what year you truck is..  it might also be equipped with an MAF sensor.. this is a sensor in the intake someplace to measure the amount of airflow into the engine so the computer can control the fuel mixture..

there are also oxygen sensors in the exhaust that really don't like to be submerged also..

next.. check the engine oil...   is it clean still.. not all milky.. where water got into a breather???

check the transmission fluid..  it should be nice clear  red..
not pink like a strawberry nesquick milk drink..

you WILL NEED to service the rear and front Differentials..   the oil will need to be drained.. and fresh gear oil installed..

if you have disc brakes.. you can hose them off..  drum brakes.. depending on how muddy the water.. you might hose them out also ..

grease the drive shaft U joints..

grease the steering linkage..