i think we may be looking too far into this.
does it by chance sound like an exhaust leak? water could have gotten on the headers and cracked them. other than that, chances are your CAI has an oil-based filter, thus is it much more difficult for water to get into the engine. Obviously anything can happen, but even if a small amount of water did get in, it probably just cleaned your cylinder walls after the combustion cycle turned it into a steam-bath...
pull the plugs, check for water, fuel, broken or damaged plugs, etc. etc. etc.
inspect the headers.
other than that, i doubt you "blewed up yer ford" by slashing in a little water.
how much water are we talking? enough to dunk the filter? just a regular ol' puddle? a small lake?