Similar threads would be something about 'washed engine and now won't run correct'.
Generally when the engine (DOHC) and water are involved, the problem will be water in the spark plug wells.
Pull the spark plug wires at the valve cover and check for water. If you find some, remove as much as you can. That should help some if not sure the problem altogether.
I've not heard of water getting into a good ignition coil/wire connection. If it has made it's way in there odds are the plug wires are bad or the coil is cracked. In both cases replace with Motorcraft parts (believe I seen we have a new Ford Parts sponsor, check their prices first).
Don't "think outside the box".
There is no box.
Do it correct, or do it twice.