Until you dump the oil, the situation wont get better and is continually doing damage. You may still have two gallons of muddy water in the crankcase. Dump the oil, pull the plugs, turn it over and let is sit with the plugs out over night. The water and/or moisture may be throwing codes that might go away, once things dry out. Pop a plug off the ECU and see if it has water or condensation trapped in it. I believe they're o-ringed, so you may be good there. If is does though, pull them all and spray with WD40. Also pop the lid off of the fuse box, it likely filled up as well. Once you get good oil in it and running, check the tranny fluid and see if it looks high or has any tiny bubbles on the stick. Probably should change it as well. Then you can start chasing the codes as long as you didn't bend a rod. You should be feeling a new vibration and likely a miss if a rod got tweaked. Crossing my fingers for you