In addition to what everyone else suggested, I would also start to go through all the electrical connections, fuses, plugs, etc. that the water could have touched. Take each one off/apart, spray compressed air to blow the water out, and coat them with dielectric grease. If you don't do this chances are you will start having 'electrical' issues at some point down the road when everything dries and gets nice and crusty.
If there was no water in the cylinders then you may have saved the engine. As pwgsx indicated running it on the hose like you did probably wore the carbon ring down. I would pull back the rubber boot and have a look, post some pictures. If worn it could cause performance issues or even let water back into the boat leading to flooding again. I would be vigilant and keep an eye on this seal next time you drop the boat into the water