i have found the problem with my 2001 f250 5.4 that i have been fighting with for a long time. it seems the gasket right above the left side of the engine has been leaking when it rains. water fills up and leaks on the coil on plugs and gets water down around the boots and shorts the coils to ground.
Fix is to remove wiper blades, remove cowls starting on the left side. remove old gasket and replace with a neoprene water prof gasket and install. remove all the coils and dry out Spark plug holes .
happy happy happy