Unfortunately the first thing you should have done was pull all the plugs and turn it over. If you had water in the cylinders it would have hydro-locked the engine. This will cause all kinds of internal problems. It ran which is a good sign, but still might be in need of some serious overhaul. If your electrical connections got soaked it could be as simple as pulling the connectors apart and using some die electric grease in them. If you ever find yourself in this spot again follow these steps first, 1. pull all the plugs (remember firing order), 2. crank the engine (water will come out the plug holes), 3. replace plugs (after your sure all the water is out) and re-start your engine. This was the main reason I put a snorkel on my Explorer (poor fresh air intake placement). It doesn't get any water in it now....