Yesterday I left my 1998 Subaru Legacy Outback EJ25 engine outside while it was raining. The intake manifold was removed at the time. The air intakes were completely full of water except one, my friend and I tipped the whole thing upside down to drain most of the water, I then sprayed copious amounts of WD40 into each intake. 3 intakes had standing WD40 in them and the other seemed to drain past the valves or something.

 

Now, what is my next step? I was not planning on removing the heads, but that might be a good idea to try and dry things out?

I would use a portable air compressor with an air nozzle attachment to force out any remaining water in the ports. If you want to go further remove the spark plugs and then crank the engine over to force out any water that may have gotten into the cylinders. You may also want to change the oil after you get the engine running again and it has gotten hot enough to evaporate any remaining water inside the engine. I would not remove the heads unless they had gasket issues.