Considering that I have a stock intake, and that the filter was dry, I am going to say hydrolock is out. Additionally, I don't think the car would idle smooth with a bad cylinder.
I am going to run some fuel treatment in it tonight with 5 gallons of fresh gas (pretty much empty now).
I am also going to disconnect the cat, and see if that improves anything. I can't explain how running a 150K mile cat through some standing water would ruin it, but I have a feeling it can. Additionally, checking for flow out of the tail pipe, there is none. There is some steam from the condensation, but no pressure what so ever...